From 3d3c5d5403346e01ca6df21f7e3c6d3edfa3cca8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 29 Sep 2022 03:41:42 +0000
Subject: [PATCH 01/77] chore(deps-dev): update pytest-cov requirement

Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest-cov/releases)
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v3.0.0...v4.0.0)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 34fdf521..170ddcac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ selenium = ">=4.2.0, <4.3.0"
 [tool.poetry.dev-dependencies]
 pre-commit = ">=2.19.0,<2.19.1"
 pytest = ">=7.1.2,<7.1.3"
-pytest-cov = ">=3.0.0,<3.0.1"
+pytest-cov = ">=3.0.0,<4.0.1"
 black = ">=22.3.0,<22.4.0"
 flake8 = ">=4.0.1,<4.1.0"
 pytest-xdist = "^2.5.0"

From f90d26ba9b667c16161cf2c3931c042bec4a6179 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 14:41:42 +0200
Subject: [PATCH 02/77] fix: add auto-release

---
 .github/workflows/release.yml | 23 +++++++++++++++++++++++
 pyproject.toml                |  9 +++++++++
 2 files changed, 32 insertions(+)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 00000000..139e0067
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,23 @@
+name: Semantic Release
+
+on:
+  push:
+    branches:
+      - main 
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    concurrency: release
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Python Semantic Release
+      uses: relekang/python-semantic-release@v7.32.0
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        # Remember to copy the tool.semantic_release section from pyproject.toml 
+        # as well
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index d9baefd8..f3cfc77d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -77,4 +77,13 @@ known_third_party = ["wandb"]
 [tool.mypy]
 ignore_missing_imports = true
 
+[tool.semantic_release]
+branch = "main"
+version_variable = [
+    "pyproject.toml:version"
+]
+upload_to_pypi = false
+upload_to_release = true
+build_command = "pip install poetry && poetry build"
+
 [tool.pyright]
\ No newline at end of file

From 96610c8848331992cb894fbfd3344aba4c57a4d9 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 14:42:38 +0200
Subject: [PATCH 03/77] fix: remove unused line in PR template

---
 .github/pull_request_template.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 3fb56546..7a97c26f 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -1,5 +1,4 @@
 - [ ] I have battle-tested on Overtaci (RMAPPS1279)
-- [ ] I have bumped the version as described in the [wiki](https://www.notion.so/Setting-up-Poetry-on-your-local-machine-76647d75e8fa4d9ba553cbc2a49946d9#dca1e0f2ce934a49acd1851aaf882d75)
 - [ ] I have assigned ranges (e.g. `>=0.1, <0.2`) to all new dependencies
 
 ## Notes for reviewers

From b45b231fa3081ccc642b4ae60869812730ccd1f2 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 14:43:50 +0200
Subject: [PATCH 04/77] fix: linting

---
 pyproject.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f3cfc77d..64e8c31d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,10 +62,6 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.semantic_release]
-version_variable = [
-    "pyproject.toml:version"
-]
 branch = "main"
 upload_to_pypi = false
 upload_to_release = true

From c85da0f5b51e48632d03c699a1b12e7cb78470bb Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 14:49:09 +0200
Subject: [PATCH 05/77] fix: incorrect placement of section

---
 pyproject.toml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 64e8c31d..da53533e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,11 +62,6 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-branch = "main"
-upload_to_pypi = false
-upload_to_release = true
-build_command = "poetry build"
-
 [tool.isort]
 known_third_party = ["wandb"]
 

From b647157dfc99703a7c1ff873def1b9c9c1cd32a5 Mon Sep 17 00:00:00 2001
From: semantic-release <semantic-release>
Date: Thu, 29 Sep 2022 15:07:39 +0200
Subject: [PATCH 06/77] 0.1.0

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 170 +++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml |   2 +-
 2 files changed, 171 insertions(+), 1 deletion(-)
 create mode 100644 CHANGELOG.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 00000000..965a93fb
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,170 @@
+# Changelog
+
+<!--next-version-placeholder-->
+
+## v0.1.0 (2022-09-29)
+### Feature
+* Add binary threshold option for `model_performance` ([`528d3a0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/528d3a0de432d607bd9528911b9cf877818aaa71))
+* Add MB PAT for auto-approval ([`d933498`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/d9334982b7431d3ae887ef4fef8aacdd53ceb8de))
+* Add automerge for dependabot PRs ([`5b1c962`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5b1c9621152b933c33dc14d2f8a389b4d644bacd))
+* Migrate `model_performance` to T2D ([`a161d30`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a161d300a57c3566f715ddb67f66e87d1c683568))
+* Add ranges to pr_template and dependencies ([`74124bc`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/74124bcc7c753b7b5a34f0e4688dc196c574ea1a))
+* Add dependabot ([`a8e3c08`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a8e3c08be4ff42485d347dbb279ec725741e0cb6))
+* Add script to train (multiple) models, sync the best to wandb, and move wandb runs to an archive folder ([`6cb63db`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/6cb63db1d1d96ebe22692001d02d0ea868016ffb))
+* Add PROJECT_ROOT_DIR ([`e915a19`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e915a19d9f29ff13e3916c9c0be7696eaa63be86))
+* Remove stop-on-concurrency ([`38f9b81`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/38f9b81fe0026420614f55e41a2ffce02c05294b))
+* Invalidate cache for $HOME as well ([`bf4afde`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/bf4afdedc964d9f58dce45094d2f75ea381e0724))
+* Make WandB log to disk then upload in batch ([`f5f6121`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f5f6121f13a172a541edcc790c362c355f4592ba))
+* Example for extra evaluation from model predictions ([`547fa8d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/547fa8db426f5e434ff34c031f9c5cf215e5ee22))
+* Save model evaluation to disk ([`4ff1fea`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4ff1fead9413f7bb917ced9150be48635f2609f0))
+* Update loader to take csv ([`1050b5e`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1050b5e29a0ac46b301578d6749d64670ec5decc))
+* Update dependencies ([`1a1b459`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1a1b459e153d48175ed298e349df962244ed4047))
+* Log feature importance table ([`f783d2a`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f783d2a443495aa8c50d8906b4be259d5cdae065))
+* Feature importance for ebm ([`cca0f6d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/cca0f6dfcb93e9ead5d2f67359317da636486d87))
+* Add mean warning days ([`5a61611`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5a61611ca4be6974b1942c2735b85deb332ccadc))
+* Split testing_project into overtaci and integration for github actions ([`d1a3221`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/d1a3221c696d1da5e952a9ee8a1853b8321af9f1))
+* Add plots to evaluate_model ([`fe627f6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/fe627f65a2a1fb7b261fbf483938cf1866daf26f))
+* Check if we can skip poetry install ([`8310cdb`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8310cdb41e0f7e4900e29efaeb8cf7e9b61f9b6c))
+* Parralelise pytest on github actions only ([`c5ce87b`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c5ce87b581d9eafd9425a1469193f041f1c57912))
+* Integration testing conf independent of overtaci_testing ([`24a22b3`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/24a22b30cf17a56d78c1666b975ecc6ef61b5e8a))
+* Add tests ([`bf77f4a`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/bf77f4a385cfe7a65e776eebd05e3d771894fdd3))
+* Add remaining plots and tests ([`c3789b0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c3789b00c00af24ee85458b4d9f0d0bf28cf794f))
+* Add heatmap ([`0acf651`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0acf651ad6a445d1b5682529c1f6c523771d3812))
+* Run pytest in parallel ([`a80dcf4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a80dcf4e7da01ead6040fb22427d32267f8bf5e2))
+* Add cache versioning ([`29d456c`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/29d456c71b0dce0ce57bd84ba465cf03d469cc4e))
+* Add flag for GPU training of xgboost ([`1027250`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/102725092705d72f36b2cefe11e0907604bbdb5b))
+* Even faster caching, hopefully ([`e8314b6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e8314b6af0166dbd993473c76f70feb0ee663d2b))
+* Add more caching ([`603c3c6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/603c3c6fb1694117ca743250e5c57cb97a174fef))
+* Added naive bayes ([`a635b2c`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a635b2c9d405172385ef08b9041d4c9d42151438))
+* Added explainable boosting machine ([`5a9aafb`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5a9aafbd6fdf505af618d9505944c901009ced05))
+* Added explainable boosting machine ([`c6d8582`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c6d8582ff130cbb3ae1f3301b329d9f8fef631a8))
+* Added z-score-normalization ([`a2faa12`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a2faa1246fff289f6dfe215d1f7a6d505b7da00f))
+* Add sensitivity_by_time_to_outcome ([`0afba8a`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0afba8a7c9169f3e4c0ae4690428dbe6bd335c8c))
+* Add logistic regression ([`28a9fb6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/28a9fb63d82bbc736c65f7ad9d1a40b09600b582))
+* Added NAs to synth data generation ([`44b679d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/44b679df7df736a8e3d807d68844dbb389033569))
+* Working parallelisation 🤘 ([`f283a0b`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f283a0b608b03ddb786c4b1e0be0872a332f7fbf))
+* Add better default params for xgboost ([`eb7d2a7`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/eb7d2a7c69e144c0f05bc9159509f4de74b56dc0))
+* :rocket: compose configs ([`f9783d1`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f9783d1a1619ecc64094fa7c94256e320306caa0))
+* Add confusion matrix to performance_by_threshold ([`e1cb42c`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e1cb42c4e4697b52c857101bb4d579791883cdbb))
+* True_prevalence, positive and negative rate to performance by threshold ([`2c85067`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2c85067978f68e23791e741780a332815dab753d))
+* Add timestamp and timestamp_outcome to synth_pred_data ([`2d22172`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2d221723a66b7e53c2be91d78635e09208ef16c3))
+* Add basic pipeline test ([`a62ab76`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a62ab76693faa2b2e6436bd92b334f1722b5a670))
+* Add option for CV or not ([`4b27123`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4b271230897c860ea6eeb063b71e852454189a60))
+* Performance by threshold table ([`390fcf0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/390fcf0bf737ea51e95aec4886b7f21f2a6ca825))
+* Ignore init with isort and ignore unused imports in init ([`45ad9e9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/45ad9e9d548b61dca0280b975d2ae3d1854e6ac9))
+* Log performance metrics ([`678bc37`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/678bc37cd1ff096eeaf380fa38865b118d34a29a))
+* Migrate to new package structure, upgrade ([`c114d19`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c114d1930d4a9e5a4a7d982068ac86399ca7c814))
+* Migrate to new package structure, upgrade ([`cd8390a`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/cd8390a8f169385922fc5ce9acbd9903a2ad2aa9))
+* Add cache to pytest ([`85e1dc4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/85e1dc4794c48ebd38f9f03271907151d8f26ec8))
+
+### Fix
+* Renamed dependency ([`e73734e`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e73734e37c705b100d52efc35223e1526262d2f9))
+* Bug if `ModelPerformance` used without id2label ([`b928ab7`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/b928ab7085454b450256dd81bf4ba916f635d17e))
+* Improvements from review ([`1d88ea0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1d88ea07763e1333debe35f516f3ac4d03acc556))
+* Invalid placement of version key for poetry install ([`52fbebe`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/52fbebeb091e4ae18b3c34ace4503865a7944ad9))
+* Update documentation of GA. ([`70442fe`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/70442fe4f68db97ac5d184ab80f170441051046c))
+* Allow duplication of small utils ([`2c1b043`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2c1b043be4e4ef57690bc04f40f3ad59926c37a2))
+* Ensure cache depends on python-version ([`1052caf`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1052caf1742f65f2075901e6756ef5404ee2224a))
+* Overspecified python 3.9.0 slowing down pytest ([`aa14654`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/aa14654491e6aedf2c88fc90ea87f3c90a99bfe7))
+* Typo in pytest ([`8ca7a3b`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8ca7a3b610c8f6221b596a1568619c4c573d4fa1))
+* Altair_saver requires selenium <4.3.0 ([`eb99574`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/eb99574d70eb0b81cc88a90bbcdceb80e9eda0a9))
+* Minor test changes ([`a3f1f5f`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a3f1f5fa04a5f5c95325f25c10644fe3b2cdab5f))
+* Remove interpret to avoid llvmlite ([`36f1d01`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/36f1d01b18442304568bc6882f943197919e7226))
+* Misspecified types ([`94e5fd4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/94e5fd4edf7efbe5b894fdf3053dee2ef6d44208))
+* Another typo in .toml, remove darglint as dep ([`df34e1b`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/df34e1b584a3d14e93d92d6c5fb97fb321b27d77))
+* Typo in toml ([`57d3d02`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/57d3d02e933736090f920bd52739c101f4f5fce2))
+* Spelling error in toml ([`8d67ded`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8d67ded228faa3969404c3e19adc7df23c6466f7))
+* Fix failing tests ([`f06ac16`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f06ac168c96239f4bbfe1d23a8759cb5ae346230))
+* Type in .venv sourcing ([`d154d13`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/d154d137c3338bb8a7bb91ab31c7b975dff9e401))
+* Remove unix-specific github actions runs ([`e000a90`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e000a90eaef76770fa1201b4d894142db4904da7))
+* Minor fixes ([`3505e70`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3505e70d1bdc5209bbfa6bdd7890d1f012b340e3))
+* Remove mypy type ignores ([`ae66393`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/ae66393c5b98b9b5f5c8191cde8fa015c4a81a2f))
+* Succesful training on overtaci ([`8e84c4b`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8e84c4b7acb6bd00f3225bdd99007d1a557ca4e7))
+* Minor changes ([`2222141`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/22221418decc9177f4eef7e04b6bd1f635c4430d))
+* Failing tests ([`1c5ace1`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1c5ace15a1aba370a5051753c8a65964238cd973))
+* Clean darglint ([`41d5565`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/41d556562e84b204b7fcf4a5f57f09d7ca9eb77f))
+* Rename github action ([`35f3dd5`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/35f3dd571c2b79da33d5bac49356084f7f0463ac))
+* Update t2d outcome ([`0bda7bd`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0bda7bd778da42bc206ee09b819957878ae1ef47))
+* Failed import ([`885c8e2`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/885c8e25c6569f1a5802bc1a837cd427c4c4e23e))
+* Wrong direction of bool ([`f8ed7f3`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f8ed7f3e8676ba7ee74f78919f2d31a38c480f16))
+* Sort feature importance plot ([`cbe81b3`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/cbe81b305b62fee9f876110eb76a773b004bf703))
+* Change argsort direction ([`19d635d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/19d635d88f022ddf5a651ce0dbb82d895b7dd4a3))
+* Control n features to plot ([`0e7bc23`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0e7bc23cff5283efbde54852231959195c923c5a))
+* Skip feature_importances_ for ebm ([`be1c8d4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/be1c8d46756e4ea029ecdcf4477fedf4709a44a8))
+* Check if array exists ([`edabb56`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/edabb5675e1a4c82f244e3d275cc6cc254b6a221))
+* Refer to correct test project on overtaci ([`b4210d8`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/b4210d8e3b271842792ef107d3071a9cfe799763))
+* Add mean_warning_days to test ([`283a6cc`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/283a6cca3049be8b91d4735f8ce9637d2a977d1d))
+* Add mean_warning_days to test ([`c2dc20f`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c2dc20fc9faa91078d128a64f02d17becf0e33f7))
+* Incorrect calculation of warning days per false positive ([`235e404`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/235e404120666dacccd7f24ed74832a5a1ae85cd))
+* Add chromedriver to GH actions ([`ce9478d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/ce9478d916cf64a417a6d712c39a2aff22dcaca1))
+* Update tests ([`3bc6873`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3bc68735b93497cced9dc05f196a692cce80d519))
+* Round decimals to percent ([`cdb3346`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/cdb3346a977a6b2f3a57e106c169d3c300ea64f3))
+* Remove pytest.ini ([`d041a16`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/d041a1664e9643145c54d9dcf6aa9af8b7356fb4))
+* Return nan if only 1 class in AUC calculation ([`17c1380`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/17c1380925e5404902b060fb1e2243fb393a6614))
+* Scale y-labels to whole numbers, e.g. 0.5 -> 50% ([`9d3ca8f`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/9d3ca8f1ccc1870d15bf2d0fd973281a83257010))
+* Config_naming ([`874a564`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/874a56497e5c686bfe040efbd8f03b80ab969201))
+* We must install poetry ([`f2474e6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f2474e6537b64a9d87020091ed41cf498aedbd8c))
+* Enable newline interpretation for pytest.ini ([`25f0026`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/25f00261624e516f7392de42df1bb155a082d750))
+* Try another way of parralising ([`5fcec4d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5fcec4d4a0a84845061b034ca3ee4a71d09bc147))
+* Remove plot saving ([`5c6819c`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5c6819c289593163dad1137a89f309ccc197a3e4))
+* Tentative fix of warning_days ([`1bf99e5`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1bf99e558cd5615a7ffe8d21da51608f98901510))
+* Remove pytest parallelisation, slows down locally ([`05cfc37`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/05cfc37bb56ed2631d3af1088ae127eff103ddea))
+* Titling of legend ([`884e08d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/884e08d8365c2cce161eb0b6989c9e3a70448ab3))
+* Cleanup ([`c7d1fb0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c7d1fb0647d924cbda40b4387c732ac1eb029a64))
+* Set known_third_party for wandb ([`4cc0ec7`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4cc0ec7b68cdd6d7813ce14e7792122c1d6a410c))
+* Caching ([`b587b14`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/b587b1473df6bf531c2536a66cc63bdea6ca2485))
+* Handle ebm on arm ([`dccd3ce`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/dccd3ce3d3804b4255a3c9fd636f8ea165effc8a))
+* Apply recommendations ([`306bdb9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/306bdb93b91cadd90bf9a3359df08340ee54af66))
+* Apply recommendations ([`c85fb55`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c85fb55aaf305817824eba13352399513973d6a9))
+* Create figures folder if it doesn't exist ([`0a86e29`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0a86e29446c32b73027f5f4b9fee9bdb0d5de865))
+* Add folder to save html to in tests ([`4323e83`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4323e83557e73de6af87ec6837208ed9b94a7471))
+* Downgrade selenium since altair uses deprecated api ([`2ba94a2`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2ba94a2d14d52a7bac1452da99f4b4df304294b4))
+* Fixed bug when there is NAs in the pred_timestamps ([`2df71fe`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2df71fe438537742cb0e71e161914e641f829c46))
+* Update config for test ([`5f16eef`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5f16eef882d228a982047b826099f2d5cc9ff389))
+* Simplify configs ([`f9cee28`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/f9cee28f326fcff854275b2c0bf56c2b02de0ab8))
+* Hyperparameters sweep works ([`5ac5f1a`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5ac5f1a17ce3d7661ffa9f019b84707f7fcb5ba7))
+* Working example ([`9f66d23`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/9f66d23e2cba94961deccd72249d92b52bc05449))
+* First working example ([`0e52681`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0e52681a1ed0e8e80348e9eb4d710b0dc9fccc3e))
+* Wandb testing with dryrun ([`142b2cc`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/142b2ccbbe1160109b619918e3d9e41b26e208b9))
+* Remove random gitignore strings ([`6c42c23`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/6c42c230af21251bb5e8f072395c6d7e2e150936))
+* Random gitnogre string ([`c289822`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c289822a4d958d75848dd78b70f8e07c89a45a57))
+* Dependencies fixed ([`81d2740`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/81d274075b7c5f32e2d95f41c0a5532a23c74968))
+* Set upper bounds for packages ([`b91026e`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/b91026ee7827acd0ba0629849214855d7b6fc0fe))
+* Add support for wandb_run dryrun ([`9e227cd`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/9e227cd06e90cb84a8f9247d35dd0c1ba1874b30))
+* Tests not passing ([`af9ecb9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/af9ecb988b1bcba1b2a279d8b820bd29d1ed13a2))
+* Remove " in test_basic_pipeline.yaml ([`c1b5b22`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c1b5b223a247017135597a18571cd7945dab4340))
+* Remove " from yaml config ([`8693d14`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8693d1452dc1c4222fc131e4b41847952a8099de))
+* Failing tests ([`21e3397`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/21e339723266121ba9f7c6faba1fdc0ed27ba295))
+* Bugs in performance_by_threshold ([`8ddd71d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8ddd71db15d61610c41053751f66789f91c5ae67))
+* Bugs ([`3506541`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3506541fe154a85dd715929086d7719d7e105a5b))
+* Update synth_prediction_data ([`3808757`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3808757a4f81b24d49b0bf0693d272a4bec62deb))
+* Generalise flatten_nested_dict ([`521baf0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/521baf0b3f21f041025da770340b621fcae5a30c))
+* Check caching ([`afb16e9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/afb16e980814de44bf1bbbf1d49d5bb5c12e4dbb))
+* Ga pytest not caching dependencies ([`fad35e9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/fad35e9e5de75dd16c9ac7077ebc1d4e40a54ce1))
+* Ignore .csv again ([`6a9a764`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/6a9a7645bee7c0ca50023c7556c3e48105e6da1b))
+* Add fake data files ([`4fbcab9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4fbcab912efed3772d9ea178283419c668c81cd8))
+* Tests not passing ([`b78dc20`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/b78dc201b574108d1481a1c95faff3a4e93db995))
+* Failing tests due to path rename ([`8407307`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8407307dad4e6e412df7c7de9fddf37dba1edf15))
+* First train with synth data ([`a4195ee`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a4195ee31f1ffec758cc0dc9e9ba9402df2db033))
+* Run on all examples ([`7795e06`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/7795e0623773838571fb07ac10d93a8d1b4ea32e))
+* Working version! ([`5f803f4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/5f803f43e5702c425db0396e8986f306151ac7b8))
+* Test MVP ([`d92b6be`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/d92b6be09b6d86993e9179c054d248d950365cec))
+* Add misc corrections ([`a17fce7`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a17fce71940307cf34b1c3002cac23ed1b54e375))
+* Basic version working ([`b1d5e10`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/b1d5e101a40722528214cbcb30b983554c9349f7))
+* Misc ([`fa6a8ba`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/fa6a8baabb93953879f5492536443b46050290eb))
+* Use pyproject.toml for poetry github action caching ([`db1e542`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/db1e54280c0b309cdc33cc4db5e481cc8d951483))
+* Update dependencies ([`41cff75`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/41cff754ebebd9172298922fa7816251d640bc97))
+* Update poetry.lock ([`4cd40bb`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4cd40bbdb40a8f3b76cd2d83d2af80b64bd76243))
+* Improve from Lasse's comments ([`528864d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/528864df3264d4014d629f54ed86f6f369ff61c6))
+* Keyerror on test ([`83bc031`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/83bc031909dfc05672b2e196db83526678a40e48))
+* Remove ambiguous comment ([`a4413bc`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a4413bc25e00e46e6a178b6ec4be86170adedf62))
+* Update pytest version ([`44eb8d5`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/44eb8d5359e4bbf1e0a3a403b8353780a7aca1b2))
+
+### Documentation
+* Add missing docstrings ([`664c8d3`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/664c8d34d9aef246c44f4b325405bf65ebd45d33))
+* Some info on feature importance ([`a22a325`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a22a325f1c2a739189c1250411654035202b8f6c))
+* Expand local chromedriver set up ([`348cb70`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/348cb7043f7e8e1e23a3d9814e06e63684baf22b))
+* Fix links to chromedriver ([`4032a79`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4032a791daeec84e03d9200888fc1badd4baae3e))
+* Installing chromedriver ([`7c40ea4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/7c40ea4d7af9090e8bf7a28b7bdb6bb620d2b13d))
+* Update docstring ([`8231659`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8231659041ad7b3883edb97ac41112ef5dd687b0))
+* Updated train model introduction ([`6fe1353`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/6fe1353918ece9a152ab00f40c90e089dd7ca4d2))
diff --git a/pyproject.toml b/pyproject.toml
index d9baefd8..0da50cd8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.2"
+version = "0.1.0"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From af89cdd96a90db3305f0087cd2e8347cc3b1821d Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 15:10:41 +0200
Subject: [PATCH 07/77] fix: bump release version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c0ed0e6d..6a56be92 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.0"
+version = "0.2.0"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 8fcb3f8703ea57697e5f89d4aaf799aec3559ff6 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:11:59 +0200
Subject: [PATCH 08/77] fix: bump release version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6a56be92..c0ed0e6d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.2.0"
+version = "0.1.0"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 4b90e57e0642b5d92d3359fbe68a5bdefd827468 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:17:24 +0200
Subject: [PATCH 09/77] fix: bump version after more lenient branch protections


From fe07436759b1a03bdc7c9eb738506e5f674c3d0c Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:30:48 +0200
Subject: [PATCH 10/77] fix: bump version after even more lenient branch
 protections


From 3e7806880598722b7a9d5200e649aa0aca7d1984 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:32:57 +0200
Subject: [PATCH 11/77] fix: bump version after more lenient branch protections
 v4


From c231bc3dda115062ce9ad94840bf36e6a8a1d395 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:33:10 +0200
Subject: [PATCH 12/77] fix: bump version after more lenient branch protections
 v4


From eb8a8c8695e4baad5d214561faf203ed1a7c50dc Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 13:34:06 +0000
Subject: [PATCH 13/77] 0.1.1

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 9 +++++++++
 pyproject.toml | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 965a93fb..fa10b9aa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,15 @@
 
 <!--next-version-placeholder-->
 
+## v0.1.1 (2022-09-29)
+### Fix
+* Bump version after more lenient branch protections v4 ([`c231bc3`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c231bc3dda115062ce9ad94840bf36e6a8a1d395))
+* Bump version after more lenient branch protections v4 ([`3e78068`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3e7806880598722b7a9d5200e649aa0aca7d1984))
+* Bump version after even more lenient branch protections ([`fe07436`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/fe07436759b1a03bdc7c9eb738506e5f674c3d0c))
+* Bump version after more lenient branch protections ([`4b90e57`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4b90e57e0642b5d92d3359fbe68a5bdefd827468))
+* Bump release version ([`8fcb3f8`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/8fcb3f8703ea57697e5f89d4aaf799aec3559ff6))
+* Bump release version ([`af89cdd`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/af89cdd96a90db3305f0087cd2e8347cc3b1821d))
+
 ## v0.1.0 (2022-09-29)
 ### Feature
 * Add binary threshold option for `model_performance` ([`528d3a0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/528d3a0de432d607bd9528911b9cf877818aaa71))
diff --git a/pyproject.toml b/pyproject.toml
index c0ed0e6d..785b38aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.0"
+version = "0.1.1"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 6b1170de1fcd04958afbb21fecbfd631e8e73517 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:37:20 +0200
Subject: [PATCH 14/77] fix: try using personal access token to override

---
 .github/workflows/bump-version.yml | 14 ++++++++++++++
 .github/workflows/release.yml      |  2 +-
 2 files changed, 15 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/bump-version.yml

diff --git a/.github/workflows/bump-version.yml b/.github/workflows/bump-version.yml
new file mode 100644
index 00000000..806788f5
--- /dev/null
+++ b/.github/workflows/bump-version.yml
@@ -0,0 +1,14 @@
+# GitHub action to check if pre-commit has been run. Runs from .pre-commit-config.yaml, where the pre-commit actions are.
+
+name: run-pre-commit
+
+on:
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/action@v3.0.0
\ No newline at end of file
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 139e0067..4aed6e83 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -18,6 +18,6 @@ jobs:
     - name: Python Semantic Release
       uses: relekang/python-semantic-release@v7.32.0
       with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
+        github_token: ${{ MB_PERSONAL_ACCESS_TOKEN}}
         # Remember to copy the tool.semantic_release section from pyproject.toml 
         # as well
\ No newline at end of file

From 0c7d7938672e25b992f3d3d358098699a66eb14b Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:37:50 +0200
Subject: [PATCH 15/77] fix: typo in release.yml

---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 4aed6e83..45d20467 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -18,6 +18,6 @@ jobs:
     - name: Python Semantic Release
       uses: relekang/python-semantic-release@v7.32.0
       with:
-        github_token: ${{ MB_PERSONAL_ACCESS_TOKEN}}
+        github_token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN}}
         # Remember to copy the tool.semantic_release section from pyproject.toml 
         # as well
\ No newline at end of file

From 1aa2dd07f7103f2573eb9991d0bab5194c4fa253 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:41:09 +0200
Subject: [PATCH 16/77] fix: bump version after more lenient branch protections
 v4


From a90f4b0e42b8458c8db1728fb4925dc9edd08b13 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:52:54 +0200
Subject: [PATCH 17/77] fix: bump version after more lenient branch protections
 v5


From 55c3acff60c892dd6b3f32ffeb0539f6eddd87a0 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:54:26 +0200
Subject: [PATCH 18/77] fix: bump version after more lenient branch protections
 v6


From 05d04b4a4ed8667c90ecc3b6ace566a571a4b70d Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 15:55:46 +0200
Subject: [PATCH 19/77] fix: bump version after more lenient branch protections
 v7


From c58e6c396ecfedd3a30a5ca2d47772d3a6d28355 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 13:56:42 +0000
Subject: [PATCH 20/77] 0.1.2

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 9 +++++++++
 pyproject.toml | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fa10b9aa..238bfd2f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,15 @@
 
 <!--next-version-placeholder-->
 
+## v0.1.2 (2022-09-29)
+### Fix
+* Bump version after more lenient branch protections v7 ([`05d04b4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/05d04b4a4ed8667c90ecc3b6ace566a571a4b70d))
+* Bump version after more lenient branch protections v6 ([`55c3acf`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/55c3acff60c892dd6b3f32ffeb0539f6eddd87a0))
+* Bump version after more lenient branch protections v5 ([`a90f4b0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/a90f4b0e42b8458c8db1728fb4925dc9edd08b13))
+* Bump version after more lenient branch protections v4 ([`1aa2dd0`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1aa2dd07f7103f2573eb9991d0bab5194c4fa253))
+* Typo in release.yml ([`0c7d793`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/0c7d7938672e25b992f3d3d358098699a66eb14b))
+* Try using personal access token to override ([`6b1170d`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/6b1170de1fcd04958afbb21fecbfd631e8e73517))
+
 ## v0.1.1 (2022-09-29)
 ### Fix
 * Bump version after more lenient branch protections v4 ([`c231bc3`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/c231bc3dda115062ce9ad94840bf36e6a8a1d395))
diff --git a/pyproject.toml b/pyproject.toml
index 785b38aa..da53533e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.1"
+version = "0.1.2"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 3af0ae6c4303d69235acfd0f4f929406068210d4 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 16:04:03 +0200
Subject: [PATCH 21/77] fix: add PAT to checkout for it to persist for python
 semantic release

---
 .github/workflows/release.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 45d20467..aa642cfa 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -14,6 +14,7 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
+        token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
 
     - name: Python Semantic Release
       uses: relekang/python-semantic-release@v7.32.0

From 240a8f453382a83d878f0aa176332674b9f3d613 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Thu, 29 Sep 2022 14:05:03 +0000
Subject: [PATCH 22/77] 0.1.3

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 4 ++++
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 238bfd2f..d35bc180 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 <!--next-version-placeholder-->
 
+## v0.1.3 (2022-09-29)
+### Fix
+* Add PAT to checkout for it to persist for python semantic release ([`3af0ae6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3af0ae6c4303d69235acfd0f4f929406068210d4))
+
 ## v0.1.2 (2022-09-29)
 ### Fix
 * Bump version after more lenient branch protections v7 ([`05d04b4`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/05d04b4a4ed8667c90ecc3b6ace566a571a4b70d))
diff --git a/pyproject.toml b/pyproject.toml
index da53533e..df3b0ff4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.2"
+version = "0.1.3"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From cd6d699c8522d0812ec5ee96b75126b7dafcb04f Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Thu, 29 Sep 2022 16:22:51 +0200
Subject: [PATCH 23/77] ci: document how to add pypi

---
 .github/workflows/release.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index aa642cfa..d3a642e9 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -11,6 +11,7 @@ jobs:
     concurrency: release
 
     steps:
+    # Checkout action is required for token to persist
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
@@ -21,4 +22,10 @@ jobs:
       with:
         github_token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN}}
         # Remember to copy the tool.semantic_release section from pyproject.toml 
-        # as well
\ No newline at end of file
+        # as well
+        # To enable pypi, 
+        # 1) Set upload_to_pypi to true in pyproject.toml and
+        # 2) Set the pypi_token in the repo
+        # 3) Uncomment the two lines below
+        # repository_username: __token__
+        # repository_password: ${{ secrets.PYPI_TOKEN }}
\ No newline at end of file

From 942fd50cdc01bec06bca9895c51dbf80a60728ed Mon Sep 17 00:00:00 2001
From: Lasse Hansen <lasseh0310@gmail.com>
Date: Thu, 29 Sep 2022 16:45:28 +0200
Subject: [PATCH 24/77] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 61440203..cde00153 100644
--- a/README.md
+++ b/README.md
@@ -52,7 +52,7 @@ To do that:
 **Work locally**
 1. Write your plot function in an appropriate file in the `psycopt2d > visualization` directory. 
 2. Test the plot on synthetic prediction data. Write a test in `tests>name_of_your_plot.py`. 
-    Use the `evaluate_saved_model_predictions.py` script as a guide.
+    Use the `evaluate_saved_model_predictions.py` script or the other visualization tests as a guide.
 
 **Work remotely**
 

From 10a3047109f71054f641a44bfda05ad884e55878 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:16:15 +0200
Subject: [PATCH 25/77] ci: test automerge with MartinBernstorff

---
 .github/workflows/dependabot_automerge.yml | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/dependabot_automerge.yml b/.github/workflows/dependabot_automerge.yml
index 677646e9..43707afc 100644
--- a/.github/workflows/dependabot_automerge.yml
+++ b/.github/workflows/dependabot_automerge.yml
@@ -11,15 +11,23 @@ permissions:
 jobs:
   dependabot-automerge:
     runs-on: ubuntu-latest
-    if: ${{ github.actor == 'dependabot[bot]'}}    
+    if: ${{ github.actor == 'MartinBernstorff'}}    
+    # if: ${{ github.actor == 'dependabot[bot]'}}    
     
     steps:
+    # Checkout action is required for token to persist
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+        token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
+
     - name: Enable auto-merge for Dependabot PRs
       run: gh pr merge --auto --merge "$PR_URL" # Use Github CLI to merge automatically the PR
       env:
         PR_URL: ${{github.event.pull_request.html_url}}
         GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-
+    
     - name: Auto approve dependabot PRs
-      if: github.actor == 'dependabot[bot]'
+      if: github.actor == 'MartinBernstorff'
+      # if: github.actor == 'dependabot[bot]'
       uses: hmarr/auto-approve-action@v2

From 78ec2cb24eabd63905200a17cdf51a0a1bff8fa2 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:16:41 +0200
Subject: [PATCH 26/77] ci: add test before release

---
 .github/workflows/main_test_and_release.yml | 78 +++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 .github/workflows/main_test_and_release.yml

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
new file mode 100644
index 00000000..74f8d0f4
--- /dev/null
+++ b/.github/workflows/main_test_and_release.yml
@@ -0,0 +1,78 @@
+name: Semantic Release
+
+on:
+  push:
+    branches:
+      - main 
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: [3.9]
+
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      ### Caching
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.1.15
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2.1.6
+        with:
+          path: |
+            .venv
+            poetry.lock
+          # Cache the complete venv dir for a given os, python version, pyproject.toml
+          key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
+
+      ### Installing
+      - name: Install Project
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install -vvv
+      
+      ### Run tests
+      - name: Run pytest
+        run: |
+          poetry run pytest --cov=src --cov-report term-missing --color=yes
+
+
+  release:
+    runs-on: ubuntu-latest
+    concurrency: release
+    needs: test
+
+    steps:
+    # Checkout action is required for token to persist
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+        token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
+
+    - name: Python Semantic Release
+      uses: relekang/python-semantic-release@v7.32.0
+      with:
+        github_token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN}}
+        # Remember to copy the tool.semantic_release section from pyproject.toml 
+        # as well
+        # To enable pypi, 
+        # 1) Set upload_to_pypi to true in pyproject.toml and
+        # 2) Set the pypi_token in the repo
+        # 3) Uncomment the two lines below
+        # repository_username: __token__
+        # repository_password: ${{ secrets.PYPI_TOKEN }}
\ No newline at end of file

From 79b00ce1977a639d068de11c2f24d77710a1dfee Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:16:58 +0200
Subject: [PATCH 27/77] ci: split ci for PRs and main

---
 .github/workflows/release.yml                 | 31 -------------------
 .../workflows/{pytest.yml => test_prs.yml}    |  6 ----
 2 files changed, 37 deletions(-)
 delete mode 100644 .github/workflows/release.yml
 rename .github/workflows/{pytest.yml => test_prs.yml} (88%)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
deleted file mode 100644
index d3a642e9..00000000
--- a/.github/workflows/release.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: Semantic Release
-
-on:
-  push:
-    branches:
-      - main 
-
-jobs:
-  release:
-    runs-on: ubuntu-latest
-    concurrency: release
-
-    steps:
-    # Checkout action is required for token to persist
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-        token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
-
-    - name: Python Semantic Release
-      uses: relekang/python-semantic-release@v7.32.0
-      with:
-        github_token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN}}
-        # Remember to copy the tool.semantic_release section from pyproject.toml 
-        # as well
-        # To enable pypi, 
-        # 1) Set upload_to_pypi to true in pyproject.toml and
-        # 2) Set the pypi_token in the repo
-        # 3) Uncomment the two lines below
-        # repository_username: __token__
-        # repository_password: ${{ secrets.PYPI_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/pytest.yml b/.github/workflows/test_prs.yml
similarity index 88%
rename from .github/workflows/pytest.yml
rename to .github/workflows/test_prs.yml
index a84cbd3b..e12825c7 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/test_prs.yml
@@ -1,7 +1,5 @@
 name: CI Pytest
 on:
-  push:
-    branches: [ main, dev ]
   pull_request:
     branches: [ main, dev ]
 
@@ -23,10 +21,6 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v3
 
-    ## setup chromedriver for saving Altair plots
-    - name: setup-chromedriver
-      uses: nanasess/setup-chromedriver@v1.0.7
-
     ### Caching
     - name: Install Poetry
       uses: snok/install-poetry@v1

From e708d6479287c76133c2becc13d43b84b91d0abe Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:19:08 +0200
Subject: [PATCH 28/77] fix: automerge with MB PAT

---
 .github/workflows/dependabot_automerge.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dependabot_automerge.yml b/.github/workflows/dependabot_automerge.yml
index 43707afc..93aa9c97 100644
--- a/.github/workflows/dependabot_automerge.yml
+++ b/.github/workflows/dependabot_automerge.yml
@@ -25,7 +25,7 @@ jobs:
       run: gh pr merge --auto --merge "$PR_URL" # Use Github CLI to merge automatically the PR
       env:
         PR_URL: ${{github.event.pull_request.html_url}}
-        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        GITHUB_TOKEN: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
     
     - name: Auto approve dependabot PRs
       if: github.actor == 'MartinBernstorff'

From 19b62306b1cb974d7ce7277dbd395e4629171e61 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Fri, 30 Sep 2022 07:20:06 +0000
Subject: [PATCH 29/77] 0.1.4

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 4 ++++
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d35bc180..6d21e41b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 <!--next-version-placeholder-->
 
+## v0.1.4 (2022-09-30)
+### Fix
+* Automerge with MB PAT ([`e708d64`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e708d6479287c76133c2becc13d43b84b91d0abe))
+
 ## v0.1.3 (2022-09-29)
 ### Fix
 * Add PAT to checkout for it to persist for python semantic release ([`3af0ae6`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/3af0ae6c4303d69235acfd0f4f929406068210d4))
diff --git a/pyproject.toml b/pyproject.toml
index df3b0ff4..024d7e1e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.3"
+version = "0.1.4"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 4638a64c4b7f59152483eb91b41730ea51aa43cf Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:22:25 +0200
Subject: [PATCH 30/77] fix: only run automerge for dependabot PRs

---
 .github/workflows/dependabot_automerge.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/dependabot_automerge.yml b/.github/workflows/dependabot_automerge.yml
index 93aa9c97..e1a352ef 100644
--- a/.github/workflows/dependabot_automerge.yml
+++ b/.github/workflows/dependabot_automerge.yml
@@ -11,8 +11,7 @@ permissions:
 jobs:
   dependabot-automerge:
     runs-on: ubuntu-latest
-    if: ${{ github.actor == 'MartinBernstorff'}}    
-    # if: ${{ github.actor == 'dependabot[bot]'}}    
+    if: ${{ github.actor == 'dependabot[bot]'}}    
     
     steps:
     # Checkout action is required for token to persist
@@ -28,6 +27,5 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
     
     - name: Auto approve dependabot PRs
-      if: github.actor == 'MartinBernstorff'
-      # if: github.actor == 'dependabot[bot]'
+      if: github.actor == 'dependabot[bot]'
       uses: hmarr/auto-approve-action@v2

From 82feb25502f06e08d65e026d545be3240dd4d94b Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Fri, 30 Sep 2022 07:32:46 +0000
Subject: [PATCH 31/77] 0.1.5

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 4 ++++
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d21e41b..e2150af7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 <!--next-version-placeholder-->
 
+## v0.1.5 (2022-09-30)
+### Fix
+* Only run automerge for dependabot PRs ([`4638a64`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4638a64c4b7f59152483eb91b41730ea51aa43cf))
+
 ## v0.1.4 (2022-09-30)
 ### Fix
 * Automerge with MB PAT ([`e708d64`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e708d6479287c76133c2becc13d43b84b91d0abe))
diff --git a/pyproject.toml b/pyproject.toml
index 024d7e1e..1ed1671c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.4"
+version = "0.1.5"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From fb2dfd07ab4efbd47cc79fc1bff6592ce04c4698 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:38:41 +0200
Subject: [PATCH 32/77] ci: don't invalidate cache because of version bump

---
 .github/workflows/dependabot_automerge.yml  | 2 +-
 .github/workflows/main_test_and_release.yml | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/dependabot_automerge.yml b/.github/workflows/dependabot_automerge.yml
index e1a352ef..99a475eb 100644
--- a/.github/workflows/dependabot_automerge.yml
+++ b/.github/workflows/dependabot_automerge.yml
@@ -28,4 +28,4 @@ jobs:
     
     - name: Auto approve dependabot PRs
       if: github.actor == 'dependabot[bot]'
-      uses: hmarr/auto-approve-action@v2
+      uses: hmarr/auto-approve-action@v2
\ No newline at end of file
diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 74f8d0f4..584adbf9 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -31,6 +31,12 @@ jobs:
           virtualenvs-create: true
           virtualenvs-in-project: true
 
+      - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
+        id: remove-version-from-toml
+        run: |
+          sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
+          cat pyproject.toml
+
       - name: Load cached venv
         id: cached-poetry-dependencies
         uses: actions/cache@v2.1.6

From 2cbd2b7c160dbf86c385d252ccf9b415f78e73fe Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:39:58 +0200
Subject: [PATCH 33/77] fix: version bump shouldn't invalidate cache in PRs

---
 .github/workflows/test_prs.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index e12825c7..34d11868 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -22,6 +22,12 @@ jobs:
       uses: actions/checkout@v3
 
     ### Caching
+    - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
+      id: remove-version-from-toml
+      run: |
+        sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
+        cat pyproject.toml
+
     - name: Install Poetry
       uses: snok/install-poetry@v1
       with:

From 7699cf8bc06db47a48f59bfd310c88f756d16c69 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:49:13 +0200
Subject: [PATCH 34/77] ci: only remove version number on ubuntu

---
 .github/workflows/main_test_and_release.yml | 1 +
 .github/workflows/test_prs.yml              | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 584adbf9..461e7d04 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -33,6 +33,7 @@ jobs:
 
       - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
         id: remove-version-from-toml
+        if: ${{ matrix.os }} == "ubuntu-latest"
         run: |
           sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
           cat pyproject.toml
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 34d11868..59fdf4d5 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -24,6 +24,7 @@ jobs:
     ### Caching
     - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
       id: remove-version-from-toml
+      if: ${{ matrix.os }} == "ubuntu-latest"
       run: |
         sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
         cat pyproject.toml

From 12c8c3385826da774ca7ebb54650cd5e543af797 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:58:02 +0200
Subject: [PATCH 35/77] ci: try again with removing version for cache

---
 .github/workflows/main_test_and_release.yml | 4 ++--
 .github/workflows/test_prs.yml              | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 461e7d04..30d5bfe8 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -1,4 +1,4 @@
-name: Semantic Release
+name: Test and release main
 
 on:
   push:
@@ -33,7 +33,7 @@ jobs:
 
       - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
         id: remove-version-from-toml
-        if: ${{ matrix.os }} == "ubuntu-latest"
+        if: matrix.os == "ubuntu-latest"
         run: |
           sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
           cat pyproject.toml
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 59fdf4d5..c7d85b0b 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -24,7 +24,7 @@ jobs:
     ### Caching
     - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
       id: remove-version-from-toml
-      if: ${{ matrix.os }} == "ubuntu-latest"
+      if: matrix.os == "ubuntu-latest"
       run: |
         sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
         cat pyproject.toml

From dcd43321fcd4eacbb7b3ba6e6f2697e4cad8bde6 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 09:58:39 +0200
Subject: [PATCH 36/77] ci: another attempt at removing version bump

---
 .github/workflows/main_test_and_release.yml | 2 +-
 .github/workflows/test_prs.yml              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 30d5bfe8..09dad3ce 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -33,7 +33,7 @@ jobs:
 
       - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
         id: remove-version-from-toml
-        if: matrix.os == "ubuntu-latest"
+        if: matrix.os == 'ubuntu-latest'
         run: |
           sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
           cat pyproject.toml
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index c7d85b0b..05965921 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -24,7 +24,7 @@ jobs:
     ### Caching
     - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
       id: remove-version-from-toml
-      if: matrix.os == "ubuntu-latest"
+      if: matrix.os == 'ubuntu-latest'
       run: |
         sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
         cat pyproject.toml

From d844c5a9b3f0f7b70d8b967a25328f967d2ee7cc Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Fri, 30 Sep 2022 08:04:57 +0000
Subject: [PATCH 37/77] 0.1.6

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 4 ++++
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e2150af7..e5b906b1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 <!--next-version-placeholder-->
 
+## v0.1.6 (2022-09-30)
+### Fix
+* Version bump shouldn't invalidate cache in PRs ([`2cbd2b7`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2cbd2b7c160dbf86c385d252ccf9b415f78e73fe))
+
 ## v0.1.5 (2022-09-30)
 ### Fix
 * Only run automerge for dependabot PRs ([`4638a64`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/4638a64c4b7f59152483eb91b41730ea51aa43cf))
diff --git a/pyproject.toml b/pyproject.toml
index 1ed1671c..c7f59ecf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.5"
+version = "0.1.6"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 9a4422a954c7092090811fa480424da6b5084567 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:06:59 +0200
Subject: [PATCH 38/77] ci: cache poetry installation

---
 .github/workflows/main_test_and_release.yml | 10 +++++++
 .github/workflows/test_prs.yml              | 29 ++++++++++++++-------
 2 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 09dad3ce..1f586cd8 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -48,6 +48,16 @@ jobs:
           # Cache the complete venv dir for a given os, python version, pyproject.toml
           key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
 
+      - name: Load cached .local (Poetry install location)
+        id: cached-poetry-dependencies
+        if: matrix.os == 'ubuntu-latest' | matrix.os == 'macos-latest'
+        uses: actions/cache@v2.1.6
+        with:
+          path: |
+            ~/.local/
+          # Cache the complete venv dir for a given os, python version, pyproject.toml
+          key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/test_prs.yml') }}
+
       ### Installing
       - name: Install Project
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 05965921..6d5ebbe9 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -13,6 +13,7 @@ jobs:
         python-version: [3.9]
         
     steps:
+    ### Setup prerequisites
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
@@ -28,14 +29,7 @@ jobs:
       run: |
         sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
         cat pyproject.toml
-
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: 1.1.15
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-
+    
     - name: Load cached venv
       id: cached-poetry-dependencies
       uses: actions/cache@v2.1.6
@@ -45,8 +39,25 @@ jobs:
           poetry.lock
         # Cache the complete venv dir for a given os, python version, pyproject.toml
         key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
+    
+    - name: Load cached .local (Poetry install location)
+      id: cached-poetry-dependencies
+      if: matrix.os == 'ubuntu-latest' | matrix.os == 'macos-latest'
+      uses: actions/cache@v2.1.6
+      with:
+        path: |
+          ~/.local/
+        # Cache the complete venv dir for a given os, python version, pyproject.toml
+        key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/test_prs.yml') }}
+
+    # Installing
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        version: 1.1.15
+        virtualenvs-create: true
+        virtualenvs-in-project: true
 
-    ### Installing
     - name: Install Project
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       run: poetry install -vvv

From c31f0850d6fe6a105590d5eb201856a997767ab4 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:07:20 +0200
Subject: [PATCH 39/77] ci: poetry cache should depend on workflow
 specification

---
 .github/workflows/main_test_and_release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 1f586cd8..6d42fd15 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -56,7 +56,7 @@ jobs:
           path: |
             ~/.local/
           # Cache the complete venv dir for a given os, python version, pyproject.toml
-          key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/test_prs.yml') }}
+          key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/main_test_and_release.yml') }}
 
       ### Installing
       - name: Install Project

From 06ffdb9c2f18e74ae248469469d0f5c8e4c8bc0f Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:08:08 +0200
Subject: [PATCH 40/77] ci: fix duplicate identifier

---
 .github/workflows/main_test_and_release.yml | 2 +-
 .github/workflows/test_prs.yml              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 6d42fd15..5a80860e 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -49,7 +49,7 @@ jobs:
           key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
 
       - name: Load cached .local (Poetry install location)
-        id: cached-poetry-dependencies
+        id: cached-poetry
         if: matrix.os == 'ubuntu-latest' | matrix.os == 'macos-latest'
         uses: actions/cache@v2.1.6
         with:
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 6d5ebbe9..7df918e4 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -41,7 +41,7 @@ jobs:
         key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
     
     - name: Load cached .local (Poetry install location)
-      id: cached-poetry-dependencies
+      id: cached-poetry
       if: matrix.os == 'ubuntu-latest' | matrix.os == 'macos-latest'
       uses: actions/cache@v2.1.6
       with:

From 6a23cab2d2db5f2023c277750e49890ed76b0eee Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:09:47 +0200
Subject: [PATCH 41/77] ci: fix 'or' specification

---
 .github/workflows/main_test_and_release.yml | 2 +-
 .github/workflows/test_prs.yml              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 5a80860e..b9bfbffc 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -50,7 +50,7 @@ jobs:
 
       - name: Load cached .local (Poetry install location)
         id: cached-poetry
-        if: matrix.os == 'ubuntu-latest' | matrix.os == 'macos-latest'
+        if: matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest' # && is 'or' for some reason
         uses: actions/cache@v2.1.6
         with:
           path: |
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 7df918e4..1141ae39 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -42,7 +42,7 @@ jobs:
     
     - name: Load cached .local (Poetry install location)
       id: cached-poetry
-      if: matrix.os == 'ubuntu-latest' | matrix.os == 'macos-latest'
+      if: matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest' # && is 'or' for some reason
       uses: actions/cache@v2.1.6
       with:
         path: |

From 489301bd8924658ebce0e6dcbee8f4161d0361f7 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:11:31 +0200
Subject: [PATCH 42/77] ci: move poetry cache before poetry install

---
 .github/workflows/main_test_and_release.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index b9bfbffc..06e88ed2 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -24,12 +24,6 @@ jobs:
         uses: actions/checkout@v3
 
       ### Caching
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.1.15
-          virtualenvs-create: true
-          virtualenvs-in-project: true
 
       - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
         id: remove-version-from-toml
@@ -59,6 +53,13 @@ jobs:
           key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/main_test_and_release.yml') }}
 
       ### Installing
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.1.15
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
       - name: Install Project
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install -vvv

From 12b3c93cc229ceec300464a1ccfe2e62be8e2f32 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:12:56 +0200
Subject: [PATCH 43/77] ci: cache .local on ubuntu OR macos

---
 .github/workflows/main_test_and_release.yml | 2 +-
 .github/workflows/test_prs.yml              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 06e88ed2..8f77efd8 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Load cached .local (Poetry install location)
         id: cached-poetry
-        if: matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest' # && is 'or' for some reason
+        if: (matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest') # && is 'or' for some reason
         uses: actions/cache@v2.1.6
         with:
           path: |
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 1141ae39..0277535c 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -42,7 +42,7 @@ jobs:
     
     - name: Load cached .local (Poetry install location)
       id: cached-poetry
-      if: matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest' # && is 'or' for some reason
+      if: (matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest') # && is 'or' for some reason
       uses: actions/cache@v2.1.6
       with:
         path: |

From 55ce611ef4389cb8abda9f87fa16088ce43c2970 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:14:40 +0200
Subject: [PATCH 44/77] ci: macos OR ubuntu, && -> ||

---
 .github/workflows/main_test_and_release.yml | 2 +-
 .github/workflows/test_prs.yml              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 8f77efd8..1f368fd4 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Load cached .local (Poetry install location)
         id: cached-poetry
-        if: (matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest') # && is 'or' for some reason
+        if: (matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest')
         uses: actions/cache@v2.1.6
         with:
           path: |
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 0277535c..a5f365b7 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -42,7 +42,7 @@ jobs:
     
     - name: Load cached .local (Poetry install location)
       id: cached-poetry
-      if: (matrix.os == 'ubuntu-latest' && matrix.os == 'macos-latest') # && is 'or' for some reason
+      if: (matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest')
       uses: actions/cache@v2.1.6
       with:
         path: |

From 6290c6c80cc18e482dc694be4545e6897df657b9 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 10:46:27 +0200
Subject: [PATCH 45/77] ci: attempt using GITHUB_TOKEN for automerge

---
 .github/workflows/dependabot_automerge.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dependabot_automerge.yml b/.github/workflows/dependabot_automerge.yml
index 99a475eb..b61a05aa 100644
--- a/.github/workflows/dependabot_automerge.yml
+++ b/.github/workflows/dependabot_automerge.yml
@@ -18,13 +18,13 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-        token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
+        token: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Enable auto-merge for Dependabot PRs
       run: gh pr merge --auto --merge "$PR_URL" # Use Github CLI to merge automatically the PR
       env:
         PR_URL: ${{github.event.pull_request.html_url}}
-        GITHUB_TOKEN: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     
     - name: Auto approve dependabot PRs
       if: github.actor == 'dependabot[bot]'

From 1b5f5a91e89826ba1c530c82570eb4465008a506 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 13:08:42 +0200
Subject: [PATCH 46/77] feat: first CI release

---
 .github/dependabot.yml                      | 11 ++++++-----
 .github/pull_request_template.md            |  2 +-
 .github/workflows/bump-version.yml          | 14 --------------
 .github/workflows/dependabot_automerge.yml  |  9 +++------
 .github/workflows/main_test_and_release.yml | 20 +++++++++++++-------
 pyproject.toml                              |  2 +-
 6 files changed, 24 insertions(+), 34 deletions(-)
 delete mode 100644 .github/workflows/bump-version.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index bbbd43c7..2666ee2d 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -8,10 +8,11 @@ updates:
   - package-ecosystem: "pip" # See documentation for possible values
     directory: "/" # Location of package manifests
     schedule:
-      interval: "daily"
+      interval: "weekly"
       day: "monday"
-      time: "05:00"
+      time: "01:00"
       timezone: "Europe/Copenhagen"
-    reviewers: 
-      - "MartinBernstorff"
-    open-pull-requests-limit: 20
+    open-pull-requests-limit: 5 
+    commit-message:
+      prefix: "fix:"
+      include: "scope"
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 7a97c26f..651849fa 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -1,5 +1,5 @@
 - [ ] I have battle-tested on Overtaci (RMAPPS1279)
-- [ ] I have assigned ranges (e.g. `>=0.1, <0.2`) to all new dependencies
+- [ ] I have assigned ranges (e.g. `>=0.1, <0.2`) to all new dependencies (allows dependabot to keep dependency ranges wide for better compatability)
 
 ## Notes for reviewers
 Reviewers can skip X, but should pay attention to Y.
diff --git a/.github/workflows/bump-version.yml b/.github/workflows/bump-version.yml
deleted file mode 100644
index 806788f5..00000000
--- a/.github/workflows/bump-version.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-# GitHub action to check if pre-commit has been run. Runs from .pre-commit-config.yaml, where the pre-commit actions are.
-
-name: run-pre-commit
-
-on:
-  pull_request:
-
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-    - uses: pre-commit/action@v3.0.0
\ No newline at end of file
diff --git a/.github/workflows/dependabot_automerge.yml b/.github/workflows/dependabot_automerge.yml
index b61a05aa..8650d52b 100644
--- a/.github/workflows/dependabot_automerge.yml
+++ b/.github/workflows/dependabot_automerge.yml
@@ -15,11 +15,6 @@ jobs:
     
     steps:
     # Checkout action is required for token to persist
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-        token: ${{ secrets.GITHUB_TOKEN }}
-
     - name: Enable auto-merge for Dependabot PRs
       run: gh pr merge --auto --merge "$PR_URL" # Use Github CLI to merge automatically the PR
       env:
@@ -28,4 +23,6 @@ jobs:
     
     - name: Auto approve dependabot PRs
       if: github.actor == 'dependabot[bot]'
-      uses: hmarr/auto-approve-action@v2
\ No newline at end of file
+      uses: hmarr/auto-approve-action@v2
+      with: 
+        github-token: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 1f368fd4..6cc8179c 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -24,14 +24,20 @@ jobs:
         uses: actions/checkout@v3
 
       ### Caching
-
-      - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
-        id: remove-version-from-toml
+      - name: Linux, Overwrite version number from pyproject.toml, so it doesn't invalidate cache
+        id: remove-version-from-toml-macos
         if: matrix.os == 'ubuntu-latest'
         run: |
           sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
           cat pyproject.toml
 
+      - name: Mac, Overwrite version number from pyproject.toml, so it doesn't invalidate cache
+        id: remove-version-from-toml-ubuntu
+        if: matrix.os == 'macos-latest'
+        run: |
+          sed -i '' "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
+          cat pyproject.toml
+
       - name: Load cached venv
         id: cached-poetry-dependencies
         uses: actions/cache@v2.1.6
@@ -42,7 +48,7 @@ jobs:
           # Cache the complete venv dir for a given os, python version, pyproject.toml
           key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
 
-      - name: Load cached .local (Poetry install location)
+      - name: Mac, Linux, Load cached .local (Poetry install location)
         id: cached-poetry
         if: (matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest')
         uses: actions/cache@v2.1.6
@@ -80,12 +86,12 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-        token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN }}
+        token: ${{ secrets.RELEASE_BOT }}
 
     - name: Python Semantic Release
       uses: relekang/python-semantic-release@v7.32.0
-      with:
-        github_token: ${{ secrets.MB_PERSONAL_ACCESS_TOKEN}}
+      with: 
+        github_token: ${{ secrets.RELEASE_BOT }}
         # Remember to copy the tool.semantic_release section from pyproject.toml 
         # as well
         # To enable pypi, 
diff --git a/pyproject.toml b/pyproject.toml
index c7f59ecf..8067a2e6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.6"
+version = "0.0.0"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From d14a05c4e32bb6fdc4ce7195d3a932105ef258ca Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 13:19:49 +0200
Subject: [PATCH 47/77] fix: CI didn't run; match version with latest release

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8067a2e6..c7f59ecf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.0.0"
+version = "0.1.6"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From 4c89bd71b5766371f4116f4ffdf3398c5706fb03 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Fri, 30 Sep 2022 11:27:39 +0000
Subject: [PATCH 48/77] 0.2.0

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 7 +++++++
 pyproject.toml | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e5b906b1..aa578918 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,13 @@
 
 <!--next-version-placeholder-->
 
+## v0.2.0 (2022-09-30)
+### Feature
+* First CI release ([`1b5f5a9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1b5f5a91e89826ba1c530c82570eb4465008a506))
+
+### Fix
+* CI didn't run; match version with latest release ([`d14a05c`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/d14a05c4e32bb6fdc4ce7195d3a932105ef258ca))
+
 ## v0.1.6 (2022-09-30)
 ### Fix
 * Version bump shouldn't invalidate cache in PRs ([`2cbd2b7`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/2cbd2b7c160dbf86c385d252ccf9b415f78e73fe))
diff --git a/pyproject.toml b/pyproject.toml
index c7f59ecf..6a56be92 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.1.6"
+version = "0.2.0"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From e68f8cf67e805bab9c19949529cdfb8d36720186 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 14:31:02 +0200
Subject: [PATCH 49/77] ci: try centralised caching

---
 .github/workflows/main_test_and_release.yml | 36 ++-------------------
 .github/workflows/test_prs.yml              | 29 ++---------------
 2 files changed, 6 insertions(+), 59 deletions(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 6cc8179c..2b6abe85 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -24,39 +24,9 @@ jobs:
         uses: actions/checkout@v3
 
       ### Caching
-      - name: Linux, Overwrite version number from pyproject.toml, so it doesn't invalidate cache
-        id: remove-version-from-toml-macos
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
-          cat pyproject.toml
-
-      - name: Mac, Overwrite version number from pyproject.toml, so it doesn't invalidate cache
-        id: remove-version-from-toml-ubuntu
-        if: matrix.os == 'macos-latest'
-        run: |
-          sed -i '' "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
-          cat pyproject.toml
-
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2.1.6
-        with:
-          path: |
-            .venv
-            poetry.lock
-          # Cache the complete venv dir for a given os, python version, pyproject.toml
-          key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
-
-      - name: Mac, Linux, Load cached .local (Poetry install location)
-        id: cached-poetry
-        if: (matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest')
-        uses: actions/cache@v2.1.6
-        with:
-          path: |
-            ~/.local/
-          # Cache the complete venv dir for a given os, python version, pyproject.toml
-          key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/main_test_and_release.yml') }}
+      - name: Cache poetry and venv
+        id: cache-poetry-and-venv
+        uses: MartinBernstorff/cache-poetry-and-venv@latest
 
       ### Installing
       - name: Install Poetry
diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index a5f365b7..88a798bc 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -23,32 +23,9 @@ jobs:
       uses: actions/checkout@v3
 
     ### Caching
-    - name: Overwrite version number from pyproject.toml, so it doesn't invalidate cache
-      id: remove-version-from-toml
-      if: matrix.os == 'ubuntu-latest'
-      run: |
-        sed -i "s/version = \".*\"/version = \"0.0.0\"/g" pyproject.toml
-        cat pyproject.toml
-    
-    - name: Load cached venv
-      id: cached-poetry-dependencies
-      uses: actions/cache@v2.1.6
-      with:
-        path: |
-          .venv
-          poetry.lock
-        # Cache the complete venv dir for a given os, python version, pyproject.toml
-        key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}
-    
-    - name: Load cached .local (Poetry install location)
-      id: cached-poetry
-      if: (matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest')
-      uses: actions/cache@v2.1.6
-      with:
-        path: |
-          ~/.local/
-        # Cache the complete venv dir for a given os, python version, pyproject.toml
-        key: venv-${{ runner.os }}-python-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('.github/workflows/cache_version') }}--${{ hashFiles('.github/workflows/test_prs.yml') }}
+    - name: Cache poetry and venv
+      id: cache-poetry-and-venv
+      uses: MartinBernstorff/cache-poetry-and-venv@latest
 
     # Installing
     - name: Install Poetry

From 28834bad0527d99ba79dba7ca76fdcb3313aa4c8 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 15:08:59 +0200
Subject: [PATCH 50/77] ci: retry centralised cache


From c9238ea2011410d7432b8f37177afd2b996dc644 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 15:41:14 +0200
Subject: [PATCH 51/77] ci: skip unused steps, invalidate cache based on matrix

---
 .github/workflows/test_prs.yml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 88a798bc..65dd1c9d 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -11,13 +11,15 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: [3.9]
+        poetry-version: [1.1.15]
+        cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
         
     steps:
     ### Setup prerequisites
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: $ {{ matrix.python-version }}
 
     - name: Checkout repo
       uses: actions/checkout@v3
@@ -26,17 +28,21 @@ jobs:
     - name: Cache poetry and venv
       id: cache-poetry-and-venv
       uses: MartinBernstorff/cache-poetry-and-venv@latest
+      with:
+        poetry-version: ${{ matrix.poetry-version }}
+        cache-version: ${{ matrix.cache-version }}
 
     # Installing
     - name: Install Poetry
+      if: steps.cache-poetry-and-venv.outputs.poetry-cache-hit != 'true'
       uses: snok/install-poetry@v1
       with:
-        version: 1.1.15
+        version: ${{ matrix.poetry-version }}
         virtualenvs-create: true
         virtualenvs-in-project: true
 
     - name: Install Project
-      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      if: steps.cache-poetry-and-venv.outputs.venv-cache-hit != 'true'
       run: poetry install -vvv
     
     ### Run tests

From 9774d6e10f1dd28f00745accf23ec6902eef35db Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 15:42:17 +0200
Subject: [PATCH 52/77] fix: typo on CI

---
 .github/workflows/test_prs.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_prs.yml b/.github/workflows/test_prs.yml
index 65dd1c9d..b0029537 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/workflows/test_prs.yml
@@ -1,10 +1,10 @@
-name: CI Pytest
+name: test_pr
 on:
   pull_request:
     branches: [ main, dev ]
 
 jobs:
-  pytest:
+  test_pr:
     runs-on: ${{ matrix.os }}
 
     strategy:
@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: $ {{ matrix.python-version }}
+        python-version: ${{ matrix.python-version }}
 
     - name: Checkout repo
       uses: actions/checkout@v3

From 8ffdd368a5a0762a26268eb1ffe34ced897334cc Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 15:44:11 +0200
Subject: [PATCH 53/77] ci: retry centralised cache


From 316e64335ee1b14aaf1c0a02fc7aad474af7a09a Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 15:56:38 +0200
Subject: [PATCH 54/77] feat: try decomposing actions

---
 .../test_prs.yml => actions/test/action.yml}  | 38 +++++++++++--------
 .github/workflows/main_test_and_release.yml   | 35 ++++-------------
 .github/workflows/pr_test.yml                 | 25 ++++++++++++
 3 files changed, 54 insertions(+), 44 deletions(-)
 rename .github/{workflows/test_prs.yml => actions/test/action.yml} (56%)
 create mode 100644 .github/workflows/pr_test.yml

diff --git a/.github/workflows/test_prs.yml b/.github/actions/test/action.yml
similarity index 56%
rename from .github/workflows/test_prs.yml
rename to .github/actions/test/action.yml
index b0029537..f629a891 100644
--- a/.github/workflows/test_prs.yml
+++ b/.github/actions/test/action.yml
@@ -1,25 +1,31 @@
-name: test_pr
-on:
-  pull_request:
-    branches: [ main, dev ]
+name: 'Run tests'
+description: 'Run tests'
+inputs:
+  os:
+    description: "Which OS to run on"
+    required: true
+    default: 'ubuntu-latest'
+  python-version:
+    description: "Which Python version to run on"
+    required: true
+    default: 3.9
+  poetry-version:
+    description: "Which version of Poetry to install"
+    default: 1.1.15
+  cache-version:
+    description: "Cache version for invalidation"
+    default: 0.0.0
 
 jobs:
   test_pr:
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      matrix:
-        os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: [3.9]
-        poetry-version: [1.1.15]
-        cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
+    runs-on: ${{ input.os }}
         
     steps:
     ### Setup prerequisites
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: ${{ inputs.python-version }}
 
     - name: Checkout repo
       uses: actions/checkout@v3
@@ -29,15 +35,15 @@ jobs:
       id: cache-poetry-and-venv
       uses: MartinBernstorff/cache-poetry-and-venv@latest
       with:
-        poetry-version: ${{ matrix.poetry-version }}
-        cache-version: ${{ matrix.cache-version }}
+        poetry-version: ${{ inputs.poetry-version }}
+        cache-version: ${{ inputs.cache-version }}
 
     # Installing
     - name: Install Poetry
       if: steps.cache-poetry-and-venv.outputs.poetry-cache-hit != 'true'
       uses: snok/install-poetry@v1
       with:
-        version: ${{ matrix.poetry-version }}
+        version: ${{ inputs.poetry-version }}
         virtualenvs-create: true
         virtualenvs-in-project: true
 
diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 2b6abe85..a7512937 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -13,38 +13,17 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: [3.9]
+        poetry-version: [1.1.15]
+        cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
 
     steps:
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - name: Run tests
+        uses: ./.github/actions/test
         with:
+          os: ${{ matrix.os }}
           python-version: ${{ matrix.python-version }}
-
-      - name: Checkout repo
-        uses: actions/checkout@v3
-
-      ### Caching
-      - name: Cache poetry and venv
-        id: cache-poetry-and-venv
-        uses: MartinBernstorff/cache-poetry-and-venv@latest
-
-      ### Installing
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.1.15
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Install Project
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install -vvv
-      
-      ### Run tests
-      - name: Run pytest
-        run: |
-          poetry run pytest --cov=src --cov-report term-missing --color=yes
-
+          poetry-version: ${{ matrix.poetry-version }}
+          cache-version: ${{ matrix.cache-version }}
 
   release:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/pr_test.yml b/.github/workflows/pr_test.yml
new file mode 100644
index 00000000..878ac30b
--- /dev/null
+++ b/.github/workflows/pr_test.yml
@@ -0,0 +1,25 @@
+name: test_pr
+on:
+  pull_request:
+    branches: [ main, dev ]
+
+jobs:
+  test_pr:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: [3.9]
+        poetry-version: [1.1.15]
+        cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
+        
+    steps:
+    - name: Run tests
+      uses: ./.github/actions/test
+      with:
+        os: ${{ matrix.os }}
+        python-version: ${{ matrix.python-version }}
+        poetry-version: ${{ matrix.poetry-version }}
+        cache-version: ${{ matrix.cache-version }}
+    

From 29c5f9289453b09130673d1348affd36efbf63f8 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 15:58:07 +0200
Subject: [PATCH 55/77] fix: checkout repo before attempting to use action

---
 .github/actions/test/action.yml             | 3 ---
 .github/workflows/main_test_and_release.yml | 3 +++
 .github/workflows/pr_test.yml               | 3 +++
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
index f629a891..252a7aaa 100644
--- a/.github/actions/test/action.yml
+++ b/.github/actions/test/action.yml
@@ -27,9 +27,6 @@ jobs:
       with:
         python-version: ${{ inputs.python-version }}
 
-    - name: Checkout repo
-      uses: actions/checkout@v3
-
     ### Caching
     - name: Cache poetry and venv
       id: cache-poetry-and-venv
diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index a7512937..6159aa88 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -17,6 +17,9 @@ jobs:
         cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
 
     steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
       - name: Run tests
         uses: ./.github/actions/test
         with:
diff --git a/.github/workflows/pr_test.yml b/.github/workflows/pr_test.yml
index 878ac30b..63244b97 100644
--- a/.github/workflows/pr_test.yml
+++ b/.github/workflows/pr_test.yml
@@ -15,6 +15,9 @@ jobs:
         cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
         
     steps:
+    - name: Checkout repo
+      uses: actions/checkout@v3
+      
     - name: Run tests
       uses: ./.github/actions/test
       with:

From e668badddeb80155da0bcf26c9bd5e155b3237bb Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 16:00:18 +0200
Subject: [PATCH 56/77] fix: typo in action (input -> inputs)

---
 .github/actions/test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
index 252a7aaa..f1c3ca19 100644
--- a/.github/actions/test/action.yml
+++ b/.github/actions/test/action.yml
@@ -18,7 +18,7 @@ inputs:
 
 jobs:
   test_pr:
-    runs-on: ${{ input.os }}
+    runs-on: ${{ inputs.os }}
         
     steps:
     ### Setup prerequisites

From 612e88e92e592bcb7145ac12159161456b9cc6f4 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 16:03:27 +0200
Subject: [PATCH 57/77] fix: another attempt

---
 .github/actions/test/action.yml             | 12 +++---------
 .github/workflows/main_test_and_release.yml |  1 -
 .github/workflows/pr_test.yml               |  1 -
 3 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
index f1c3ca19..45e0fd71 100644
--- a/.github/actions/test/action.yml
+++ b/.github/actions/test/action.yml
@@ -1,10 +1,6 @@
 name: 'Run tests'
 description: 'Run tests'
 inputs:
-  os:
-    description: "Which OS to run on"
-    required: true
-    default: 'ubuntu-latest'
   python-version:
     description: "Which Python version to run on"
     required: true
@@ -16,11 +12,9 @@ inputs:
     description: "Cache version for invalidation"
     default: 0.0.0
 
-jobs:
-  test_pr:
-    runs-on: ${{ inputs.os }}
-        
-    steps:
+runs:
+  using: "composite"
+  steps:
     ### Setup prerequisites
     - name: Set up Python
       uses: actions/setup-python@v4
diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 6159aa88..c0e28a36 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -23,7 +23,6 @@ jobs:
       - name: Run tests
         uses: ./.github/actions/test
         with:
-          os: ${{ matrix.os }}
           python-version: ${{ matrix.python-version }}
           poetry-version: ${{ matrix.poetry-version }}
           cache-version: ${{ matrix.cache-version }}
diff --git a/.github/workflows/pr_test.yml b/.github/workflows/pr_test.yml
index 63244b97..39179639 100644
--- a/.github/workflows/pr_test.yml
+++ b/.github/workflows/pr_test.yml
@@ -21,7 +21,6 @@ jobs:
     - name: Run tests
       uses: ./.github/actions/test
       with:
-        os: ${{ matrix.os }}
         python-version: ${{ matrix.python-version }}
         poetry-version: ${{ matrix.poetry-version }}
         cache-version: ${{ matrix.cache-version }}

From 35745779716151b6e3f90e5a1b93023a27943603 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 16:05:25 +0200
Subject: [PATCH 58/77] fix: specify shell

---
 .github/actions/test/action.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
index 45e0fd71..c38e0f47 100644
--- a/.github/actions/test/action.yml
+++ b/.github/actions/test/action.yml
@@ -40,9 +40,11 @@ runs:
 
     - name: Install Project
       if: steps.cache-poetry-and-venv.outputs.venv-cache-hit != 'true'
+      shell: bash
       run: poetry install -vvv
     
     ### Run tests
     - name: Run pytest
+      shell: bash
       run: |
         poetry run pytest --cov=src --cov-report term-missing --color=yes

From b8afd2f1ca34594e4936981cc9ca919e8f5fb3b8 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 16:14:06 +0200
Subject: [PATCH 59/77] ci: update for modified caching

---
 .github/actions/test/action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
index c38e0f47..b1b8522f 100644
--- a/.github/actions/test/action.yml
+++ b/.github/actions/test/action.yml
@@ -28,6 +28,7 @@ runs:
       with:
         poetry-version: ${{ inputs.poetry-version }}
         cache-version: ${{ inputs.cache-version }}
+        python-versoin: ${{ inputs.python-version }}
 
     # Installing
     - name: Install Poetry

From 674688248d9dc300fe307217c064cfc97f8c7422 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 16:14:40 +0200
Subject: [PATCH 60/77] ci: fix type on python-version

---
 .github/actions/test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
index b1b8522f..825b0e6e 100644
--- a/.github/actions/test/action.yml
+++ b/.github/actions/test/action.yml
@@ -28,7 +28,7 @@ runs:
       with:
         poetry-version: ${{ inputs.poetry-version }}
         cache-version: ${{ inputs.cache-version }}
-        python-versoin: ${{ inputs.python-version }}
+        python-version: ${{ inputs.python-version }}
 
     # Installing
     - name: Install Poetry

From 822ac84721962a9c03bd45810f72553f3c05dc33 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 16:16:13 +0200
Subject: [PATCH 61/77] ci: retry centralised cache


From b06034fc070a922155a5f421272be17d482ad2e3 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Fri, 30 Sep 2022 23:08:12 +0200
Subject: [PATCH 62/77] ci: improve based on comments

---
 .github/workflows/main_test_and_release.yml |  5 ++--
 .github/workflows/pr_test.yml               | 27 ---------------------
 2 files changed, 3 insertions(+), 29 deletions(-)
 delete mode 100644 .github/workflows/pr_test.yml

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index c0e28a36..cc57e1b3 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -1,6 +1,7 @@
-name: Test and release main
+name: Test (and release)
 
 on:
+  pull_request:
   push:
     branches:
       - main 
@@ -31,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     concurrency: release
     needs: test
-
+    if: github.ref == 'refs/heads/main'
     steps:
     # Checkout action is required for token to persist
     - uses: actions/checkout@v2
diff --git a/.github/workflows/pr_test.yml b/.github/workflows/pr_test.yml
deleted file mode 100644
index 39179639..00000000
--- a/.github/workflows/pr_test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: test_pr
-on:
-  pull_request:
-    branches: [ main, dev ]
-
-jobs:
-  test_pr:
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      matrix:
-        os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: [3.9]
-        poetry-version: [1.1.15]
-        cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
-        
-    steps:
-    - name: Checkout repo
-      uses: actions/checkout@v3
-      
-    - name: Run tests
-      uses: ./.github/actions/test
-      with:
-        python-version: ${{ matrix.python-version }}
-        poetry-version: ${{ matrix.poetry-version }}
-        cache-version: ${{ matrix.cache-version }}
-    

From 35af1854f9c2f681b0258ebeb414c1e64925fc26 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sat, 1 Oct 2022 15:52:20 +0200
Subject: [PATCH 63/77] Rerun tests

---
 .github/workflows/main_test_and_release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index cc57e1b3..89d8f3a1 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     concurrency: release
     needs: test
-    if: github.ref == 'refs/heads/main'
+    if: github.ref == 'refs/heads/master'
     steps:
     # Checkout action is required for token to persist
     - uses: actions/checkout@v2

From 828f954a7285cf586161bd4568cc3160c8a19980 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sun, 2 Oct 2022 16:30:46 +0200
Subject: [PATCH 64/77] Fix typo in GA, master -> main

---
 .github/workflows/main_test_and_release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 89d8f3a1..6db630e2 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     concurrency: release
     needs: test
-    if: github.ref == 'refs/heads/master'
+    if: github.ref == 'refs/head/main'
     steps:
     # Checkout action is required for token to persist
     - uses: actions/checkout@v2

From 1b644d78cd9977c81fb142f0cefc190905aa19bd Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sun, 2 Oct 2022 16:37:09 +0200
Subject: [PATCH 65/77] Invalidate cache

---
 .github/workflows/main_test_and_release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 6db630e2..af8757c5 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -15,7 +15,7 @@ jobs:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: [3.9]
         poetry-version: [1.1.15]
-        cache-version: [0.0.0] # Change this number if you want to manually invalidate all caches
+        cache-version: [0.0.1] # Change this number if you want to manually invalidate all caches
 
     steps:
       - name: Checkout repo

From 62fbd6f8104fef4ba8f8465cee1678738eb49438 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sun, 2 Oct 2022 17:21:54 +0200
Subject: [PATCH 66/77] Invalidate cache

---
 .github/workflows/main_test_and_release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index af8757c5..3c4b0620 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -15,7 +15,7 @@ jobs:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: [3.9]
         poetry-version: [1.1.15]
-        cache-version: [0.0.1] # Change this number if you want to manually invalidate all caches
+        cache-version: [0.0.2] # Change this number if you want to manually invalidate all caches
 
     steps:
       - name: Checkout repo

From 004d00cc1e8433b9bb1b4f52a79283c5de925358 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Mon, 3 Oct 2022 10:31:30 +0200
Subject: [PATCH 67/77] ci: migrate to shared test workflow

---
 .github/test/action.yml                     | 51 +++++++++++++++++++++
 .github/workflows/main_test_and_release.yml | 38 ++++-----------
 2 files changed, 61 insertions(+), 28 deletions(-)
 create mode 100644 .github/test/action.yml

diff --git a/.github/test/action.yml b/.github/test/action.yml
new file mode 100644
index 00000000..825b0e6e
--- /dev/null
+++ b/.github/test/action.yml
@@ -0,0 +1,51 @@
+name: 'Run tests'
+description: 'Run tests'
+inputs:
+  python-version:
+    description: "Which Python version to run on"
+    required: true
+    default: 3.9
+  poetry-version:
+    description: "Which version of Poetry to install"
+    default: 1.1.15
+  cache-version:
+    description: "Cache version for invalidation"
+    default: 0.0.0
+
+runs:
+  using: "composite"
+  steps:
+    ### Setup prerequisites
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    ### Caching
+    - name: Cache poetry and venv
+      id: cache-poetry-and-venv
+      uses: MartinBernstorff/cache-poetry-and-venv@latest
+      with:
+        poetry-version: ${{ inputs.poetry-version }}
+        cache-version: ${{ inputs.cache-version }}
+        python-version: ${{ inputs.python-version }}
+
+    # Installing
+    - name: Install Poetry
+      if: steps.cache-poetry-and-venv.outputs.poetry-cache-hit != 'true'
+      uses: snok/install-poetry@v1
+      with:
+        version: ${{ inputs.poetry-version }}
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+
+    - name: Install Project
+      if: steps.cache-poetry-and-venv.outputs.venv-cache-hit != 'true'
+      shell: bash
+      run: poetry install -vvv
+    
+    ### Run tests
+    - name: Run pytest
+      shell: bash
+      run: |
+        poetry run pytest --cov=src --cov-report term-missing --color=yes
diff --git a/.github/workflows/main_test_and_release.yml b/.github/workflows/main_test_and_release.yml
index 2b6abe85..2633ed2a 100644
--- a/.github/workflows/main_test_and_release.yml
+++ b/.github/workflows/main_test_and_release.yml
@@ -1,6 +1,7 @@
-name: Test and release main
+name: Test (and release)
 
 on:
+  pull_request:
   push:
     branches:
       - main 
@@ -13,44 +14,25 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: [3.9]
+        poetry-version: [1.1.15]
+        cache-version: [0.0.2] # Change this number if you want to manually invalidate all caches
 
     steps:
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
       - name: Checkout repo
         uses: actions/checkout@v3
 
-      ### Caching
-      - name: Cache poetry and venv
-        id: cache-poetry-and-venv
-        uses: MartinBernstorff/cache-poetry-and-venv@latest
-
-      ### Installing
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
+      - name: Run tests
+        uses: ./.github/actions/test
         with:
-          version: 1.1.15
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Install Project
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install -vvv
-      
-      ### Run tests
-      - name: Run pytest
-        run: |
-          poetry run pytest --cov=src --cov-report term-missing --color=yes
-
+          python-version: ${{ matrix.python-version }}
+          poetry-version: ${{ matrix.poetry-version }}
+          cache-version: ${{ matrix.cache-version }}
 
   release:
     runs-on: ubuntu-latest
     concurrency: release
     needs: test
-
+    if: ${{ github.ref == 'refs/heads/main' }}
     steps:
     # Checkout action is required for token to persist
     - uses: actions/checkout@v2

From d08c2d2096df30b25e0fd18f63c55debed6fc862 Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Mon, 3 Oct 2022 08:35:08 +0000
Subject: [PATCH 68/77] 0.3.0

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 11 +++++++++++
 pyproject.toml |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aa578918..7ce858a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,17 @@
 
 <!--next-version-placeholder-->
 
+## v0.3.0 (2022-10-03)
+### Feature
+* Try decomposing actions ([`316e643`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/316e64335ee1b14aaf1c0a02fc7aad474af7a09a))
+
+### Fix
+* Specify shell ([`3574577`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/35745779716151b6e3f90e5a1b93023a27943603))
+* Another attempt ([`612e88e`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/612e88e92e592bcb7145ac12159161456b9cc6f4))
+* Typo in action (input -> inputs) ([`e668bad`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/e668badddeb80155da0bcf26c9bd5e155b3237bb))
+* Checkout repo before attempting to use action ([`29c5f92`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/29c5f9289453b09130673d1348affd36efbf63f8))
+* Typo on CI ([`9774d6e`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/9774d6e10f1dd28f00745accf23ec6902eef35db))
+
 ## v0.2.0 (2022-09-30)
 ### Feature
 * First CI release ([`1b5f5a9`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/1b5f5a91e89826ba1c530c82570eb4465008a506))
diff --git a/pyproject.toml b/pyproject.toml
index 6a56be92..4a0b119c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.2.0"
+version = "0.3.0"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]
 

From c75743b93d681c06d68741cbf2a1fd319a5fd555 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Mon, 3 Oct 2022 14:28:37 +0200
Subject: [PATCH 69/77] ci: delete unused test action

---
 .github/test/action.yml | 51 -----------------------------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 .github/test/action.yml

diff --git a/.github/test/action.yml b/.github/test/action.yml
deleted file mode 100644
index 825b0e6e..00000000
--- a/.github/test/action.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-name: 'Run tests'
-description: 'Run tests'
-inputs:
-  python-version:
-    description: "Which Python version to run on"
-    required: true
-    default: 3.9
-  poetry-version:
-    description: "Which version of Poetry to install"
-    default: 1.1.15
-  cache-version:
-    description: "Cache version for invalidation"
-    default: 0.0.0
-
-runs:
-  using: "composite"
-  steps:
-    ### Setup prerequisites
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ inputs.python-version }}
-
-    ### Caching
-    - name: Cache poetry and venv
-      id: cache-poetry-and-venv
-      uses: MartinBernstorff/cache-poetry-and-venv@latest
-      with:
-        poetry-version: ${{ inputs.poetry-version }}
-        cache-version: ${{ inputs.cache-version }}
-        python-version: ${{ inputs.python-version }}
-
-    # Installing
-    - name: Install Poetry
-      if: steps.cache-poetry-and-venv.outputs.poetry-cache-hit != 'true'
-      uses: snok/install-poetry@v1
-      with:
-        version: ${{ inputs.poetry-version }}
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-
-    - name: Install Project
-      if: steps.cache-poetry-and-venv.outputs.venv-cache-hit != 'true'
-      shell: bash
-      run: poetry install -vvv
-    
-    ### Run tests
-    - name: Run pytest
-      shell: bash
-      run: |
-        poetry run pytest --cov=src --cov-report term-missing --color=yes

From 346368ad0a8dd013814e25941d9b6560941bc410 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Tue, 4 Oct 2022 14:07:51 +0200
Subject: [PATCH 70/77] ci: update PR template

---
 .github/pull_request_template.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 651849fa..a2475804 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -1,5 +1,6 @@
 - [ ] I have battle-tested on Overtaci (RMAPPS1279)
 - [ ] I have assigned ranges (e.g. `>=0.1, <0.2`) to all new dependencies (allows dependabot to keep dependency ranges wide for better compatability)
+- [ ] At least one of the commits is prefixed with either "fix:" or "feat:"
 
 ## Notes for reviewers
 Reviewers can skip X, but should pay attention to Y.

From 501c27383779601d9faade95b30646de393b2873 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sat, 1 Oct 2022 18:56:01 +0200
Subject: [PATCH 71/77] minor linting

---
 src/psycopt2d/evaluation.py                 | 15 +++++++--------
 src/psycopt2d/visualization/altair_utils.py |  3 ++-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/psycopt2d/evaluation.py b/src/psycopt2d/evaluation.py
index 7c21001a..5129b3f2 100644
--- a/src/psycopt2d/evaluation.py
+++ b/src/psycopt2d/evaluation.py
@@ -1,12 +1,12 @@
 """Functions for evaluating a model's prredictions."""
-from typing import Iterable, Optional
+from collections.abc import Iterable
 
 import altair as alt
 import numpy as np
 import pandas as pd
-import wandb
 from sklearn.metrics import f1_score, roc_auc_score
 from sklearn.pipeline import Pipeline
+from wandb.sdk.wandb_run import Run as wandb_run
 
 from psycopt2d.tables import generate_feature_importances_table
 from psycopt2d.tables.performance_by_threshold import (
@@ -30,7 +30,7 @@ def evaluate_model(
     y_col_name: str,
     train_col_names: Iterable[str],
     y_hat_prob_col_name: str,
-    run: Optional[wandb.run] = None,
+    run: wandb_run,
 ):
     """Runs the evaluation suite on the model and logs to WandB.
     At present, this includes:
@@ -49,8 +49,7 @@ def evaluate_model(
         y_col_name (str): Label column name
         train_col_names (Iterable[str]): Column names for all predictors
         y_hat_prob_col_name (str): Column name containing pred_proba output
-        run (Optional[wandb.run]): WandB run to log to. Will not log to WandB if
-            set to None
+        run (wandb_run): WandB run to log to.
     """
     y = eval_dataset[y_col_name]
     y_hat_probs = eval_dataset[y_hat_prob_col_name]
@@ -88,7 +87,7 @@ def evaluate_model(
             f.write(f"{run.id},{auc}\n")
 
     # Tables
-    ## Performance by threshold
+    # Performance by threshold
     performance_by_threshold_df = generate_performance_by_positive_rate_table(
         labels=y,
         pred_probs=y_hat_probs,
@@ -128,7 +127,7 @@ def evaluate_model(
         )
         run.log({"feature_importance_table": feature_importances_table})
 
-    ## Sensitivity by time to outcome
+    # Sensitivity by time to outcome
     plots.update(
         {
             "sensitivity_by_time_by_threshold": plot_sensitivity_by_time_to_outcome(
@@ -163,6 +162,6 @@ def evaluate_model(
         },
     )
 
-    ## Log all the figures to wandb
+    # Log all the figures to wandb
     for chart_name, chart_obj in plots.items():
         log_altair_to_wandb(chart=chart_obj, chart_name=chart_name, run=run)
diff --git a/src/psycopt2d/visualization/altair_utils.py b/src/psycopt2d/visualization/altair_utils.py
index 07372dd9..b99e7245 100644
--- a/src/psycopt2d/visualization/altair_utils.py
+++ b/src/psycopt2d/visualization/altair_utils.py
@@ -3,6 +3,7 @@
 
 import wandb
 from altair.vegalite.v4.api import Chart
+from wandb.sdk.wandb_run import Run as wandb_run
 
 
 def altair_chart_to_file(
@@ -32,7 +33,7 @@ def altair_chart_to_file(
     return str(filepath)
 
 
-def log_altair_to_wandb(chart: Chart, chart_name: str, run: wandb.run):
+def log_altair_to_wandb(chart: Chart, chart_name: str, run: wandb_run):  # type: ignore
     """Helper to log Altair charts.
 
     Args:

From de621e8bbdb22addae980822f0926cfd733d1e3a Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sat, 1 Oct 2022 19:16:39 +0200
Subject: [PATCH 72/77] fix: some extra linting

---
 src/psycopt2d/train_model.py | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/psycopt2d/train_model.py b/src/psycopt2d/train_model.py
index 15697ddf..d60bb630 100644
--- a/src/psycopt2d/train_model.py
+++ b/src/psycopt2d/train_model.py
@@ -1,7 +1,6 @@
 """Training script for training a single model for predicting t2d."""
 import os
 from pathlib import Path
-from typing import List, Tuple
 
 import hydra
 import numpy as np
@@ -55,6 +54,8 @@ def create_preprocessing_pipeline(cfg):
 
 
 def create_model(cfg):
+    """Instantiate and return a model object based on settings in the config
+    file."""
     model_dict = MODELS.get(cfg.model.model_name)
 
     model_args = model_dict["static_hyperparameters"]
@@ -66,7 +67,7 @@ def create_model(cfg):
     return mdl
 
 
-def load_dataset_from_config(cfg) -> Tuple[pd.DataFrame, pd.DataFrame]:
+def load_dataset_from_config(cfg) -> tuple[pd.DataFrame, pd.DataFrame]:
     """Load dataset based on settings in the config file."""
 
     allowed_data_sources = {"csv", "synthetic"}
@@ -115,12 +116,12 @@ def stratified_cross_validation(
     cfg,
     pipe: Pipeline,
     dataset: pd.DataFrame,
-    train_col_names: List[str],
+    train_col_names: list[str],
     outcome_col_name: str,
 ):
     """Performs stratified and grouped cross validation using the pipeline."""
-    X = dataset[train_col_names]
-    y = dataset[outcome_col_name]
+    X = dataset[train_col_names]  # pylint: disable=invalid-name
+    y = dataset[outcome_col_name]  # pylint: disable=invalid-name
 
     # Create folds
     folds = StratifiedGroupKFold(n_splits=cfg.training.n_splits).split(
@@ -132,7 +133,7 @@ def stratified_cross_validation(
     # Perform CV and get out of fold predictions
     dataset["oof_y_hat"] = np.nan
     for train_idxs, val_idxs in folds:
-        X_, y_ = X.loc[train_idxs], y.loc[train_idxs]
+        X_, y_ = X.loc[train_idxs], y.loc[train_idxs]  # pylint: disable=invalid-name
         pipe.fit(X_, y_)
 
         y_hat = pipe.predict_proba(X_)[:, 1]
@@ -146,11 +147,12 @@ def stratified_cross_validation(
 
 
 @hydra.main(
-    config_path=CONFIG_PATH,
+    config_path=str(CONFIG_PATH),
     config_name="default_config",
     version_base="1.2",
 )
 def main(cfg):
+    """Main function for training a single model."""
     run = wandb.init(
         project=cfg.project.name,
         reinit=True,
@@ -172,12 +174,12 @@ def main(cfg):
     pipe = Pipeline(steps)
 
     # train
-    ## define columns
-    OUTCOME_COL_NAME = (
+    # define columns
+    OUTCOME_COL_NAME = (  # pylint: disable=invalid-name
         f"outc_dichotomous_t2d_within_{cfg.data.lookahead_days}_days_max_fallback_0"
     )
 
-    TRAIN_COL_NAMES = [
+    TRAIN_COL_NAMES = [  # pylint: disable=invalid-name
         c for c in train.columns if c.startswith(cfg.data.pred_col_name_prefix)
     ]
 
@@ -187,9 +189,9 @@ def main(cfg):
         pipe["model"].feature_names = TRAIN_COL_NAMES
 
     if cfg.training.n_splits is None:  # train on pre-defined splits
-        X_train = train[TRAIN_COL_NAMES]
+        X_train = train[TRAIN_COL_NAMES]  # pylint: disable=invalid-name
         y_train = train[OUTCOME_COL_NAME]
-        X_val = val[TRAIN_COL_NAMES]
+        X_val = val[TRAIN_COL_NAMES]  # pylint: disable=invalid-name
 
         pipe.fit(X_train, y_train)
 

From 03a0be1772737379cdcb2088934f6e7666d54013 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sat, 1 Oct 2022 19:24:36 +0200
Subject: [PATCH 73/77] fix: more linting, enable pylint pre-commit hook

---
 .pre-commit-config.yaml                       | 13 ++++++++++
 src/psycopt2d/evaluation.py                   |  2 +-
 .../synth_data_generator.py                   |  1 +
 src/psycopt2d/tables/__init__.py              |  1 +
 src/psycopt2d/tables/tables.py                | 24 ++++++++++++++-----
 5 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 031bf0eb..02e37842 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -44,3 +44,16 @@ repos:
         entry: check-yaml
         language: python
         types: [yaml]
+        
+  - repo: https://github.com/pycqa/pylint
+    rev: v2.15.2
+    hooks:
+      - id: pylint
+        types: [python]
+        args:
+          [
+            "-rn", # Only display messages
+            "-sn", # Don't display the score
+            "--disable=R,import-error" # Refactors are not important enough to block a commit. 
+            # Unused-imports aren't testable by the github action, so don't test that here.
+          ]
\ No newline at end of file
diff --git a/src/psycopt2d/evaluation.py b/src/psycopt2d/evaluation.py
index 5129b3f2..f3505ecb 100644
--- a/src/psycopt2d/evaluation.py
+++ b/src/psycopt2d/evaluation.py
@@ -122,7 +122,7 @@ def evaluate_model(
         )
         # Log as table too for readability
         feature_importances_table = generate_feature_importances_table(
-            column_names=feature_names,
+            feature_names=feature_names,
             feature_importances=pipe["model"].feature_importances_,
         )
         run.log({"feature_importance_table": feature_importances_table})
diff --git a/src/psycopt2d/synth_data_generator/synth_data_generator.py b/src/psycopt2d/synth_data_generator/synth_data_generator.py
index 61a18e57..aba6e34f 100644
--- a/src/psycopt2d/synth_data_generator/synth_data_generator.py
+++ b/src/psycopt2d/synth_data_generator/synth_data_generator.py
@@ -1,3 +1,4 @@
+# TODO: Refactor this to use only be an application of module in psycop-ml-utils instead.
 from pathlib import Path
 from typing import Dict, List, Optional, Tuple, Union
 
diff --git a/src/psycopt2d/tables/__init__.py b/src/psycopt2d/tables/__init__.py
index 234ec2e1..20d4dcf2 100644
--- a/src/psycopt2d/tables/__init__.py
+++ b/src/psycopt2d/tables/__init__.py
@@ -1,2 +1,3 @@
+# pylint: disable=missing-module-docstring
 from .performance_by_threshold import generate_performance_by_positive_rate_table
 from .tables import auc_by_group_table, generate_feature_importances_table
diff --git a/src/psycopt2d/tables/tables.py b/src/psycopt2d/tables/tables.py
index dfbe1345..746af043 100644
--- a/src/psycopt2d/tables/tables.py
+++ b/src/psycopt2d/tables/tables.py
@@ -1,5 +1,7 @@
+"""Tables for evaluation of models."""
+from collections.abc import Iterable
 from functools import partial
-from typing import Iterable, List, Union
+from typing import Union
 
 import pandas as pd
 import wandb
@@ -10,7 +12,7 @@ def auc_by_group_table(
     df: pd.DataFrame,
     pred_probs_col_name: str,
     outcome_col_name: str,
-    groups: Union[List[str], str],
+    groups: Union[list[str], str],
 ) -> pd.DataFrame:
     """Create table with AUC per group.
 
@@ -19,7 +21,7 @@ def auc_by_group_table(
             and groups to stratify by.
         pred_probs_col_name (str): The column containing the predicted probabilities
         outcome_col_name (str): The column containing the labels
-        groups (Union[List[str], str]): The (categorical) groups to
+        groups (Union[list[str], str]): The (categorical) groups to
             stratify the table by.
 
     Returns:
@@ -68,13 +70,23 @@ def _calc_auc_and_n(
 
 
 def generate_feature_importances_table(
-    column_names: Iterable[str],
+    feature_names: Iterable[str],
     feature_importances: Iterable[str],
     output_format: str = "wandb_table",
-) -> Union[pd.DataFrame, str]:
+) -> Union[pd.DataFrame, wandb.Table]:
+    """Generate table with feature importances.
+
+    Args:
+        feature_names (Iterable[str]): The names of the columns to generate feature_importances for
+        feature_importances (Iterable[str]): The feature importances
+        output_format (str, optional): The output format. Takes one of "html", "df", "wandb_table". Defaults to "wandb_table".
+
+    Returns:
+        Union[pd.DataFrame, wandb.Table]: The table with feature importances
+    """
 
     df = pd.DataFrame(
-        {"predictor": column_names, "feature_importance": feature_importances},
+        {"predictor": feature_names, "feature_importance": feature_importances},
     )
     df = df.sort_values("feature_importance", ascending=False)
 

From d72b913295bee00db2592ef7a93091d803ddba22 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Sun, 2 Oct 2022 16:30:03 +0200
Subject: [PATCH 74/77] Rename List to list

---
 reports/render_report.py                      |  6 ++---
 .../evaluate_saved_model_predictions.py       | 10 ++++----
 src/psycopt2d/feature_transformers.py         | 10 ++++----
 src/psycopt2d/load.py                         |  6 ++---
 src/psycopt2d/sync_best_runs_to_wandb.py      |  4 ++--
 .../synth_data_generator.py                   | 14 +++++------
 src/psycopt2d/utils.py                        | 24 +++++++++----------
 .../visualization/feature_importance.py       |  4 ++--
 .../visualization/performance_over_time.py    |  4 ++--
 src/psycopt2d/visualization/sens_over_time.py |  8 +++----
 10 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/reports/render_report.py b/reports/render_report.py
index 0b2ca444..1c784fb8 100644
--- a/reports/render_report.py
+++ b/reports/render_report.py
@@ -6,7 +6,7 @@
 be in a dir called 'tables' and figures in a dir called 'figs'
 """
 
-from typing import List
+from typing import list
 
 import pandas as pd
 
@@ -48,11 +48,11 @@ def load_table(filepath: str):
     return df.to_markdown()
 
 
-def center_text(text: List[str]):
+def center_text(text: list[str]):
     return "\n" + f"""<div align="center">{_join_by_newline(text)}</div>"""
 
 
-def _join_by_newline(text: List[str]):
+def _join_by_newline(text: list[str]):
     return "\n\n".join(text)
 
 
diff --git a/src/psycopt2d/evaluate_saved_model_predictions.py b/src/psycopt2d/evaluate_saved_model_predictions.py
index 9a0c21d6..5fae4c72 100644
--- a/src/psycopt2d/evaluate_saved_model_predictions.py
+++ b/src/psycopt2d/evaluate_saved_model_predictions.py
@@ -9,7 +9,7 @@
 from pathlib import Path
 
 import pandas as pd
-from omegaconf.dictconfig import DictConfig
+from omegaconf.dictconfig import dictConfig
 
 from psycopt2d.utils import PROJECT_ROOT, read_pickle
 from psycopt2d.visualization import plot_auc_by_time_from_first_visit
@@ -23,20 +23,20 @@ def infer_outcome_col_name(df: pd.DataFrame):
         raise ValueError("More than one outcome inferred")
 
 
-def infer_predictor_col_names(df: pd.DataFrame, cfg: DictConfig) -> list[str]:
+def infer_predictor_col_names(df: pd.DataFrame, cfg: dictConfig) -> list[str]:
     """Get the predictors that are used in the model.
 
     Args:
         df (pd.Dataframe): Dataframe with model predictions
-        cfg (DictConfig): Config file
+        cfg (dictConfig): Config file
 
     Returns:
-        list[str]: List of predictors
+        list[str]: list of predictors
     """
     return [c for c in df.columns if c.startswith(cfg.data.pred_col_name_prefix)]
 
 
-def load_model_predictions_and_cfg(path: Path) -> tuple[pd.DataFrame, DictConfig]:
+def load_model_predictions_and_cfg(path: Path) -> tuple[pd.DataFrame, dictConfig]:
     """Load model predictions and config file from a pickle file.
 
     Args:
diff --git a/src/psycopt2d/feature_transformers.py b/src/psycopt2d/feature_transformers.py
index 7af641b1..bf318af5 100644
--- a/src/psycopt2d/feature_transformers.py
+++ b/src/psycopt2d/feature_transformers.py
@@ -1,6 +1,6 @@
 """Custom transformers for data preprocessing."""
 from datetime import datetime
-from typing import List, Optional
+from typing import Optional, list
 
 from sklearn.base import BaseEstimator, TransformerMixin
 
@@ -10,15 +10,15 @@ class ConvertToBoolean(BaseEstimator, TransformerMixin):
 
     def __init__(
         self,
-        columns_to_include: Optional[List[str]] = None,
-        columns_to_skip: Optional[List[str]] = ["age_in_years", "sex_female"],
+        columns_to_include: Optional[list[str]] = None,
+        columns_to_skip: Optional[list[str]] = ["age_in_years", "sex_female"],
         ignore_dtypes: Optional[set] = {"datetime64[ns]", "<M8[ns]"},
     ) -> None:
         """
         Args:
-            columns_to_include (List[str], optional): Columns to convert to boolean.
+            columns_to_include (list[str], optional): Columns to convert to boolean.
                 Acts as a whitelist, skipping all columns not in the list.
-            columns_to_skip (List[str], optional): Columns to not convert to boolean.
+            columns_to_skip (list[str], optional): Columns to not convert to boolean.
                 Acts as a blacklist.
                 Defaults to ["age_in_years", "male"].
                 Default to None in which case all columns are included.
diff --git a/src/psycopt2d/load.py b/src/psycopt2d/load.py
index d2afafca..f12e4d99 100644
--- a/src/psycopt2d/load.py
+++ b/src/psycopt2d/load.py
@@ -1,7 +1,7 @@
 # from datetime import date, datetime, timedelta
 from datetime import date, datetime, timedelta
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import Optional, Union, list
 
 import pandas as pd
 from psycopmlutils.sql.loader import sql_load
@@ -11,7 +11,7 @@
 
 
 def load_dataset(
-    split_names: Union[List[str], str],
+    split_names: Union[list[str], str],
     dir: Path,
     drop_patient_if_outcome_before_date: Union[datetime, str],
     min_lookahead_days: int,
@@ -21,7 +21,7 @@ def load_dataset(
     """Load dataset for t2d.
 
     Args:
-        split_names (Union[List[str], str]): Names of splits, includes "train", "val",
+        split_names (Union[list[str], str]): Names of splits, includes "train", "val",
             "test".
         dir (Path): Directory of the dataset.
         drop_patient_if_outcome_before_date (Union[datetime, str]): Remove patients which
diff --git a/src/psycopt2d/sync_best_runs_to_wandb.py b/src/psycopt2d/sync_best_runs_to_wandb.py
index 84ed1046..cf49f8da 100644
--- a/src/psycopt2d/sync_best_runs_to_wandb.py
+++ b/src/psycopt2d/sync_best_runs_to_wandb.py
@@ -19,7 +19,7 @@ def get_best_run_ids(top_n: int) -> list[str]:
         top_n (int): Number of runs to return
 
     Returns:
-        list[str]: List of run ids
+        list[str]: list of run ids
     """
     df = pd.read_csv(AUC_LOGGING_FILE_PATH)
     return df.sort_values("auc", ascending=False)["run_id"].tolist()[:top_n]
@@ -42,7 +42,7 @@ def sync_runs_to_wandb(runs: list[str], project: str) -> None:
     """Sync runs to wandb.
 
     Args:
-        runs (list[str]): List of run ids
+        runs (list[str]): list of run ids
         project (str): Project name
     """
 
diff --git a/src/psycopt2d/synth_data_generator/synth_data_generator.py b/src/psycopt2d/synth_data_generator/synth_data_generator.py
index aba6e34f..ae42ac45 100644
--- a/src/psycopt2d/synth_data_generator/synth_data_generator.py
+++ b/src/psycopt2d/synth_data_generator/synth_data_generator.py
@@ -1,6 +1,6 @@
 # TODO: Refactor this to use only be an application of module in psycop-ml-utils instead.
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -8,20 +8,20 @@
 
 
 def generate_synth_data(
-    predictors: Dict,
+    predictors: dict,
     outcome_column_name: str,
     n_samples: int,
     logistic_outcome_model: str,
     intercept: Optional[Union[int, float, complex, str, bytes]] = 0,
     na_prob: Optional[float] = 0.01,
-    na_ignore_cols: List[str] = [],
+    na_ignore_cols: list[str] = [],
     prob_outcome: Optional[float] = 0.08,
-    noise_mean_sd: Optional[Tuple[float, float]] = (0, 1),
+    noise_mean_sd: Optional[tuple[float, float]] = (0, 1),
 ) -> pd.DataFrame:
     """Takes a dict and generates synth data from it.
 
     Args:
-        predictors (Dict): A dict representing each column of shape:
+        predictors (dict): A dict representing each column of shape:
             {"col_name":
                 {
                 "column_type": str,
@@ -37,9 +37,9 @@ def generate_synth_data(
         intercept (float, optional): The intercept of the logistic outcome model. Defaults to 0.
         na_prob (float, optional): Probability of changing a value in a predictor column
             to NA.
-        na_ignore_cols (List[str], optional): Columns to ignore when creating NAs
+        na_ignore_cols (list[str], optional): Columns to ignore when creating NAs
         prob_outcome (float): Probability of a given row receiving "1" for the outcome.
-        noise_mean_sd (Tuple[float, float], optional): mean and sd of the noise.
+        noise_mean_sd (tuple[float, float], optional): mean and sd of the noise.
             Increase SD to obtain more uncertain models.
 
     Returns:
diff --git a/src/psycopt2d/utils.py b/src/psycopt2d/utils.py
index 7cc5ced1..eb6601f2 100644
--- a/src/psycopt2d/utils.py
+++ b/src/psycopt2d/utils.py
@@ -1,12 +1,12 @@
 import time
 from collections.abc import MutableMapping
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Union
+from typing import Any, Iterable, Union, dict, list
 
 import dill as pkl
 import numpy as np
 import pandas as pd
-from omegaconf.dictconfig import DictConfig
+from omegaconf.dictconfig import dictConfig
 from wasabi import msg
 
 from psycopt2d.model_performance import ModelPerformance
@@ -45,22 +45,22 @@ def format_dict_for_printing(d: dict) -> str:
 
 
 def flatten_nested_dict(
-    d: Dict,
+    d: dict,
     parent_key: str = "",
     sep: str = ".",
-) -> Dict:
+) -> dict:
     """Recursively flatten an infinitely nested dict.
 
     E.g. {"level1": {"level2": "level3": {"level4": 5}}}} becomes
     {"level1.level2.level3.level4": 5}.
 
     Args:
-        d (Dict): Dict to flatten.
+        d (dict): dict to flatten.
         parent_key (str): The parent key for the current dict, e.g. "level1" for the first iteration.
         sep (str): How to separate each level in the dict. Defaults to ".".
 
     Returns:
-        Dict: The flattened dict.
+        dict: The flattened dict.
     """
 
     items = []
@@ -111,12 +111,12 @@ def drop_records_if_datediff_days_smaller_than(
         ]
 
 
-def round_floats_to_edge(series: pd.Series, bins: List[float]) -> np.ndarray:
+def round_floats_to_edge(series: pd.Series, bins: list[float]) -> np.ndarray:
     """Rounds a float to the lowest value it is larger than.
 
     Args:
         series (pd.Series): The series of floats to round to bin edges.
-        bins (List[floats]): Values to round to.
+        bins (list[floats]): Values to round to.
 
     Returns:
         A numpy ndarray with the borders.
@@ -158,12 +158,12 @@ def calculate_performance_metrics(
     return performance_metrics
 
 
-def bin_continuous_data(series: pd.Series, bins: List[int]) -> pd.Series:
+def bin_continuous_data(series: pd.Series, bins: list[int]) -> pd.Series:
     """For prettier formatting of continuous binned data such as age.
 
     Args:
         series (pd.Series): Series with continuous data such as age
-        bins (List[int]): Desired bins
+        bins (list[int]): Desired bins
 
     Returns:
         pd.Series: Binned data
@@ -247,13 +247,13 @@ def read_pickle(path: str) -> Any:
         return pkl.load(f)
 
 
-def prediction_df_with_metadata_to_disk(df: pd.DataFrame, cfg: DictConfig) -> None:
+def prediction_df_with_metadata_to_disk(df: pd.DataFrame, cfg: dictConfig) -> None:
     """Saves prediction dataframe with and hydra config to disk. Stored as a
     dict with keys "df" and "cfg".
 
     Args:
         df (pd.DataFrame): Dataframe to save.
-        cfg (DictConfig): Hydra config.
+        cfg (dictConfig): Hydra config.
     """
     model_args = format_dict_for_printing(cfg.model)
 
diff --git a/src/psycopt2d/visualization/feature_importance.py b/src/psycopt2d/visualization/feature_importance.py
index 5c9c2238..70ea625e 100644
--- a/src/psycopt2d/visualization/feature_importance.py
+++ b/src/psycopt2d/visualization/feature_importance.py
@@ -1,4 +1,4 @@
-from typing import Iterable, List, Union
+from typing import Iterable, Union, list
 
 import altair as alt
 import numpy as np
@@ -8,7 +8,7 @@
 
 def plot_feature_importances(
     column_names: Iterable[str],
-    feature_importances: Union[List[float], np.ndarray],
+    feature_importances: Union[list[float], np.ndarray],
     top_n_feature_importances: int,
 ) -> alt.Chart:
     """Plots feature importances.
diff --git a/src/psycopt2d/visualization/performance_over_time.py b/src/psycopt2d/visualization/performance_over_time.py
index ccfcb366..16a3cbc2 100644
--- a/src/psycopt2d/visualization/performance_over_time.py
+++ b/src/psycopt2d/visualization/performance_over_time.py
@@ -3,7 +3,7 @@
 2. AUC by time from first visit
 3. AUC by time until diagnosis
 """
-from typing import Callable, Iterable, List, Optional
+from typing import Callable, Iterable, Optional, list
 
 import altair as alt
 import numpy as np
@@ -105,7 +105,7 @@ def create_performance_by_time_from_event_df(
     prediction_timestamps: Iterable[pd.Timestamp],
     metric_fn: Callable,
     direction: str,
-    bins: List[int],
+    bins: list[int],
     pretty_bins: Optional[bool] = True,
     drop_na_events: Optional[bool] = True,
 ) -> pd.DataFrame:
diff --git a/src/psycopt2d/visualization/sens_over_time.py b/src/psycopt2d/visualization/sens_over_time.py
index b948ad9a..b5623b3e 100644
--- a/src/psycopt2d/visualization/sens_over_time.py
+++ b/src/psycopt2d/visualization/sens_over_time.py
@@ -1,5 +1,5 @@
 from functools import partial
-from typing import Iterable, List
+from typing import Iterable, list
 
 import altair as alt
 import numpy as np
@@ -96,17 +96,17 @@ def create_sensitivity_by_time_to_outcome_df(
 def plot_sensitivity_by_time_to_outcome(
     labels: Iterable[int],
     y_hat_probs: Iterable[int],
-    pred_proba_thresholds: List[float],
+    pred_proba_thresholds: list[float],
     outcome_timestamps: Iterable[pd.Timestamp],
     prediction_timestamps: Iterable[pd.Timestamp],
-    bins: List[int] = [0, 28, 182, 365, 730, 1825],
+    bins: list[int] = [0, 28, 182, 365, 730, 1825],
 ):
     """Plot sensitivity by time to outcome.
 
     Args:
         labels (Iterable[int]): True labels of the data.
         y_hat_probs (Iterable[int]): Predicted probability of class 1.
-        pred_proba_thresholds (Iterable[float]): List of pred_proba thresholds to plot, above which predictions are classified as positive.
+        pred_proba_thresholds (Iterable[float]): list of pred_proba thresholds to plot, above which predictions are classified as positive.
         outcome_timestamps (Iterable[pd.Timestamp]): Timestamp of the outcome, if any.
         prediction_timestamps (Iterable[pd.Timestamp]): Timestamp of the prediction.
         bins (list, optional): Default bins for time to outcome. Defaults to [0, 1, 7, 14, 28, 182, 365, 730, 1825].

From ad4142b315cc9feaad9d07a61ad4d745a3a463ce Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Tue, 4 Oct 2022 11:14:19 +0200
Subject: [PATCH 75/77] lint: fix all pylint

---
 .pre-commit-config.yaml                       |  3 +-
 docs/conf.py                                  |  2 +-
 pyproject.toml                                | 12 ++-
 reports/render_report.py                      | 40 ++++++----
 src/psycopt2d/about.py                        |  1 +
 .../generate_synthetic_dataset_for_eval.py    | 14 ++--
 .../evaluate_saved_model_predictions.py       | 19 +++--
 src/psycopt2d/evaluation.py                   |  2 +-
 src/psycopt2d/feature_transformers.py         | 26 ++++---
 src/psycopt2d/load.py                         | 17 +++--
 src/psycopt2d/models.py                       |  6 +-
 .../synth_data_generator.py                   | 23 ++++--
 .../tables/performance_by_threshold.py        | 76 ++++++++++---------
 src/psycopt2d/train_model.py                  |  6 +-
 src/psycopt2d/utils.py                        | 22 +++---
 src/psycopt2d/visualization/__init__.py       |  1 +
 src/psycopt2d/visualization/altair_utils.py   |  1 +
 src/psycopt2d/visualization/base_charts.py    |  4 +-
 .../visualization/feature_importance.py       |  5 +-
 .../visualization/performance_over_time.py    | 15 ++--
 src/psycopt2d/visualization/prob_over_time.py |  3 +-
 src/psycopt2d/visualization/sens_over_time.py |  7 +-
 tests/conftest.py                             |  1 +
 tests/test_auc_by_group_table.py              |  1 +
 tests/test_calculate_performance_metrics.py   | 28 +++----
 tests/test_performance_by_threshold.py        | 18 +++--
 tests/test_sens_over_time.py                  | 36 ++++-----
 tests/test_train_model.py                     |  1 +
 tests/test_utils.py                           |  2 +
 tests/test_visualizations.py                  |  5 ++
 tests/utils_for_testing.py                    | 25 +++++-
 31 files changed, 259 insertions(+), 163 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 02e37842..6d75ff71 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,9 +14,10 @@ repos:
       - id: add-trailing-comma
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.37.3
+    rev: v3.0.0 
     hooks:
       - id: pyupgrade
+        args: ["--py39-plus"]
 
   - repo: https://github.com/myint/docformatter
     rev: v1.5.0
diff --git a/docs/conf.py b/docs/conf.py
index 7d96a078..b420ec84 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+# pylint: disable-all
 #
 # psycop-t2d documentation build configuration file, created by
 # sphinx-quickstart.
diff --git a/pyproject.toml b/pyproject.toml
index 4a0b119c..c135d610 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,12 +62,18 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.isort]
-known_third_party = ["wandb"]
-
 [tool.mypy]
 ignore_missing_imports = true
 
+[tool.pylint]
+load-plugins = "pylint.extensions.docparams,pylint.extensions.code_style,pylint.extensions.for_any_all,pylint.extensions.typing"
+good-names = "df,p,f,d,e,n,k,i,v,y_,X,y"
+disable = "too-many-lines,line-too-long,missing-raises-doc,no-self-argument,unused-wildcard-import,wildcard-import,no-else-return,too-many-arguments,redefined-outer-name,c-extension-no-member,wrong-import-order,import-outside-toplevel"
+extension-pkg-allow-list = "wandb"
+
+[tool.isort]
+known_third_party = ["wandb"]
+
 [tool.semantic_release]
 branch = "main"
 version_variable = [
diff --git a/reports/render_report.py b/reports/render_report.py
index 1c784fb8..77885ea3 100644
--- a/reports/render_report.py
+++ b/reports/render_report.py
@@ -6,14 +6,13 @@
 be in a dir called 'tables' and figures in a dir called 'figs'
 """
 
-from typing import list
 
 import pandas as pd
 
 from psycopt2d.utils import PROJECT_ROOT
 
 # import pandoc
-# See comment in pyproject.toml on Pandoc, not currently in use. import pandoc
+# See comment in pyproject.toml on Pandoc, not currently in use. Should work now, see: https://github.com/boisgera/pandoc/pull/49#issuecomment-1265983279
 
 AUTHORS = ["Lasse Hansen", "MB", "KCE"]
 TITLE = "Paradigm Shattering Paper 1"
@@ -25,6 +24,7 @@
 
 
 def insert_figure(line: str, fig_number: int):
+    """Add a figure to the report as md."""
     path, caption = line.split(":")
     path = path.strip().replace("{", "")
     caption = caption.strip().replace("}", "")
@@ -34,35 +34,40 @@ def insert_figure(line: str, fig_number: int):
 
 
 def insert_table(line: str, table_number: int):
+    """Add a table to the report as md."""
     path, caption = line.split(":")
     path = path.strip().replace("{", "")
     caption = caption.strip().replace("}", "")
-    md_table = load_table(path)
+    md_table = csv_to_md(path)
 
     table = f"_Table {table_number}: {caption}_\n\n{md_table}\n"
     return table
 
 
-def load_table(filepath: str):
+def csv_to_md(filepath: str):
+    """Load a table from a csv and return as markdown."""
     df = pd.read_csv(filepath)
     return df.to_markdown()
 
 
 def center_text(text: list[str]):
+    """Add html center align tags."""
     return "\n" + f"""<div align="center">{_join_by_newline(text)}</div>"""
 
 
 def _join_by_newline(text: list[str]):
+    """Join a list of strings by newline."""
     return "\n\n".join(text)
 
 
 if __name__ == "__main__":
-    with open(REPORT_PATH / "report.md", "r") as f:
+    with open(REPORT_PATH / "report.md") as f:  # pylint: disable=unspecified-encoding
         report = f.readlines()
 
-    md = []
-    fig_counter = 1
-    table_counter = 1
+    mdown_in_process = []
+    FIG_COUNT = 1
+    TABLE_COUNT = 1
+
     for line in report:
         if "@title" in line:
             line = line.replace("@title", TITLE)
@@ -70,16 +75,19 @@ def _join_by_newline(text: list[str]):
             line = line.replace("@authors", center_text(AUTHORS))
         elif line.startswith("{"):
             if "figs" in line:
-                line = insert_figure(line, fig_number=fig_counter)
-                fig_counter += 1
+                line = insert_figure(line, fig_number=FIG_COUNT)
+                FIG_COUNT += 1
             if "tables" in line:
-                line = insert_table(line, table_number=table_counter)
-                table_counter += 1
-        md.append(line)
+                line = insert_table(line, table_number=TABLE_COUNT)
+                TABLE_COUNT += 1
+        mdown_in_process.append(line)
 
-    md = "".join(md)
+    MDOWN_OUT = "".join(mdown_in_process)
     # pandoc_format = pandoc.read(md)
     # pandoc.write(pandoc_format, file=str(REPORT_PATH / "auto_report.docx"))
 
-    with open(REPORT_PATH / "auto_report.md", "w") as f:
-        f.write(md)
+    with open(  # pylint: disable=unspecified-encoding
+        REPORT_PATH / "auto_report.md",
+        "w",
+    ) as f:
+        f.write(MDOWN_OUT)
diff --git a/src/psycopt2d/about.py b/src/psycopt2d/about.py
index a316d8fc..99a76d8f 100644
--- a/src/psycopt2d/about.py
+++ b/src/psycopt2d/about.py
@@ -1,3 +1,4 @@
+# pylint: disable-all
 import pkg_resources
 
 __version__ = pkg_resources.get_distribution("psycop-t2d").version
diff --git a/src/psycopt2d/data/generate_synthetic_dataset_for_eval.py b/src/psycopt2d/data/generate_synthetic_dataset_for_eval.py
index d7f4ea09..2f199b6d 100644
--- a/src/psycopt2d/data/generate_synthetic_dataset_for_eval.py
+++ b/src/psycopt2d/data/generate_synthetic_dataset_for_eval.py
@@ -1,3 +1,4 @@
+"""Generate synthetic data for evaluation of the model."""
 import datetime as dt
 from typing import Any, Optional
 
@@ -18,7 +19,8 @@ def years_to_seconds(years):
     return years * 365 * 24 * 60 * 60
 
 
-def return_0_with_prob(prob):
+def return_0_with_prob(prob: float):
+    """Return 0 with a given probability."""
     return 0 if np.random.random() < prob else 1
 
 
@@ -72,14 +74,14 @@ def overwrite_prop_with_null(
 if __name__ == "__main__":
     msg = Printer(timestamp=True)
     base = pd.Timestamp.today()
-    n_rows = 100_000
+    N_ROWS = 100_000
 
     df = pd.DataFrame()
 
-    df["dw_ek_borger"] = [np.random.randint(0, 100_000) for n in range(n_rows)]
+    df["dw_ek_borger"] = [np.random.randint(0, 100_000) for _ in range(N_ROWS)]
 
     # Generate timestamps
-    df["timestamp"] = [base] * n_rows
+    df["timestamp"] = [base] * N_ROWS
 
     msg.info("Adding differences")
     df["time_differences"] = [
@@ -89,12 +91,12 @@ def overwrite_prop_with_null(
                 years_to_seconds(years=10),
             ),
         )
-        for n in range(n_rows)
+        for _ in range(N_ROWS)
     ]
     df["timestamp"] = df["timestamp"] + df["time_differences"]
     df.drop("time_differences", axis=1, inplace=True)
 
-    df["pred_prob"] = [(np.random.random() - 0.45) for n in range(n_rows)]
+    df["pred_prob"] = [(np.random.random() - 0.45) for _ in range(N_ROWS)]
     df["pred_prob"] = df["pred_prob"].clip(0, 1)
     df["pred"] = df["pred_prob"].clip(0, 1).round()
 
diff --git a/src/psycopt2d/evaluate_saved_model_predictions.py b/src/psycopt2d/evaluate_saved_model_predictions.py
index 5fae4c72..0505ff86 100644
--- a/src/psycopt2d/evaluate_saved_model_predictions.py
+++ b/src/psycopt2d/evaluate_saved_model_predictions.py
@@ -9,26 +9,27 @@
 from pathlib import Path
 
 import pandas as pd
-from omegaconf.dictconfig import dictConfig
+from omegaconf.dictconfig import DictConfig
 
 from psycopt2d.utils import PROJECT_ROOT, read_pickle
 from psycopt2d.visualization import plot_auc_by_time_from_first_visit
 
 
-def infer_outcome_col_name(df: pd.DataFrame):
-    outcome_name = [c for c in df.columns if c.startswith("outc")]
+def infer_outcome_col_name(df: pd.DataFrame, prefix: str = "outc_") -> str:
+    """Infer the outcome column name from the dataframe."""
+    outcome_name = [c for c in df.columns if c.startswith(prefix)]
     if len(outcome_name) == 1:
         return outcome_name[0]
     else:
         raise ValueError("More than one outcome inferred")
 
 
-def infer_predictor_col_names(df: pd.DataFrame, cfg: dictConfig) -> list[str]:
+def infer_predictor_col_names(df: pd.DataFrame, cfg: DictConfig) -> list[str]:
     """Get the predictors that are used in the model.
 
     Args:
         df (pd.Dataframe): Dataframe with model predictions
-        cfg (dictConfig): Config file
+        cfg (DictConfig): Config file
 
     Returns:
         list[str]: list of predictors
@@ -36,7 +37,7 @@ def infer_predictor_col_names(df: pd.DataFrame, cfg: dictConfig) -> list[str]:
     return [c for c in df.columns if c.startswith(cfg.data.pred_col_name_prefix)]
 
 
-def load_model_predictions_and_cfg(path: Path) -> tuple[pd.DataFrame, dictConfig]:
+def load_model_predictions_and_cfg(path: Path) -> tuple[pd.DataFrame, DictConfig]:
     """Load model predictions and config file from a pickle file.
 
     Args:
@@ -57,7 +58,9 @@ def load_model_predictions_and_cfg(path: Path) -> tuple[pd.DataFrame, dictConfig
 
     train_col_names = infer_predictor_col_names(eval_df, cfg)
     y_col_name = infer_outcome_col_name(eval_df)
-    y_hat_prob_col_name = "y_hat_prob"  # change to 'y_hat_prob_oof' if using cv
+
+    Y_HAT_PROB_COL_NAME = "y_hat_prob"  # change to 'y_hat_prob_oof' if using cv
+
     first_visit_timestamp = eval_df.groupby(cfg.data.id_col_name)[
         cfg.data.pred_timestamp_col_name
     ].transform("min")
@@ -65,7 +68,7 @@ def load_model_predictions_and_cfg(path: Path) -> tuple[pd.DataFrame, dictConfig
     # Do whatever extra evaluation you want to here
     p = plot_auc_by_time_from_first_visit(
         labels=eval_df[y_col_name],
-        y_hat_probs=eval_df[y_hat_prob_col_name],
+        y_hat_probs=eval_df[Y_HAT_PROB_COL_NAME],
         first_visit_timestamps=first_visit_timestamp,
         prediction_timestamps=eval_df[cfg.data.pred_timestamp_col_name],
     )
diff --git a/src/psycopt2d/evaluation.py b/src/psycopt2d/evaluation.py
index f3505ecb..6640087d 100644
--- a/src/psycopt2d/evaluation.py
+++ b/src/psycopt2d/evaluation.py
@@ -6,7 +6,7 @@
 import pandas as pd
 from sklearn.metrics import f1_score, roc_auc_score
 from sklearn.pipeline import Pipeline
-from wandb.sdk.wandb_run import Run as wandb_run
+from wandb.sdk.wandb_run import Run as wandb_run  # pylint: disable=no-name-in-module
 
 from psycopt2d.tables import generate_feature_importances_table
 from psycopt2d.tables.performance_by_threshold import (
diff --git a/src/psycopt2d/feature_transformers.py b/src/psycopt2d/feature_transformers.py
index bf318af5..5886d6dd 100644
--- a/src/psycopt2d/feature_transformers.py
+++ b/src/psycopt2d/feature_transformers.py
@@ -1,24 +1,26 @@
 """Custom transformers for data preprocessing."""
 from datetime import datetime
-from typing import Optional, list
+from typing import Optional
 
 from sklearn.base import BaseEstimator, TransformerMixin
 
+# pylint: disable=missing-function-docstring
+
 
 class ConvertToBoolean(BaseEstimator, TransformerMixin):
     """Convert all cells with a value to True, otherwise false."""
 
     def __init__(
         self,
-        columns_to_include: Optional[list[str]] = None,
-        columns_to_skip: Optional[list[str]] = ["age_in_years", "sex_female"],
-        ignore_dtypes: Optional[set] = {"datetime64[ns]", "<M8[ns]"},
+        columns_to_include: Optional[tuple[str]] = None,
+        columns_to_skip: Optional[tuple[str, str]] = ("age_in_years", "sex_female"),
+        ignore_dtypes: Optional[tuple] = ("datetime64[ns]", "<M8[ns]"),
     ) -> None:
         """
         Args:
             columns_to_include (list[str], optional): Columns to convert to boolean.
                 Acts as a whitelist, skipping all columns not in the list.
-            columns_to_skip (list[str], optional): Columns to not convert to boolean.
+            columns_to_skip (Union(tuple[str], None) : Columns to not convert to boolean.
                 Acts as a blacklist.
                 Defaults to ["age_in_years", "male"].
                 Default to None in which case all columns are included.
@@ -27,12 +29,12 @@ def __init__(
         """
         self.columns_to_skip = columns_to_skip
         self.columns_to_include = columns_to_include
-        self.ignore_dtypes = ignore_dtypes
+        self.ignore_dtypes = set(ignore_dtypes) if ignore_dtypes else None
 
-    def fit(self, X, y=None):
+    def fit(self, _, y=None):  # pylint: disable=unused-argument
         return self
 
-    def transform(self, X, y=None):
+    def transform(self, X, y=None):  # pylint: disable=unused-argument
         columns = X.columns
 
         if self.columns_to_include:
@@ -41,7 +43,7 @@ def transform(self, X, y=None):
         cols_to_round = [
             c
             for c in columns
-            if (X[c].dtype not in self.ignore_dtype) or c in self.columns_to_skip
+            if (X[c].dtype not in self.ignore_dtypes) or c in self.columns_to_skip
         ]
 
         for col in cols_to_round:
@@ -51,6 +53,8 @@ def transform(self, X, y=None):
 
 
 class DateTimeConverter(BaseEstimator, TransformerMixin):
+    """Convert datetime columns to integers."""
+
     valid_types = {"ordinal"}
     datetime_dtypes = {"datetime64[ns]", "<M8[ns]"}
 
@@ -72,10 +76,10 @@ def __init__(self, convert_to="ordinal"):
 
         self.convert_to = convert_to
 
-    def fit(self, X, y=None):
+    def fit(self, X, y=None):  # pylint: disable=unused-argument
         return self
 
-    def transform(self, X, y=None):
+    def transform(self, X, y=None):  # pylint: disable=unused-argument
         # extract datatime columns
         dt_columns = [c for c in X.columns if X[c].dtypes in self.datetime_dtypes]
 
diff --git a/src/psycopt2d/load.py b/src/psycopt2d/load.py
index f12e4d99..a7a4bae3 100644
--- a/src/psycopt2d/load.py
+++ b/src/psycopt2d/load.py
@@ -1,7 +1,8 @@
+"""Loader for the t2d dataset."""
 # from datetime import date, datetime, timedelta
 from datetime import date, datetime, timedelta
 from pathlib import Path
-from typing import Optional, Union, list
+from typing import Optional, Union
 
 import pandas as pd
 from psycopmlutils.sql.loader import sql_load
@@ -12,7 +13,7 @@
 
 def load_dataset(
     split_names: Union[list[str], str],
-    dir: Path,
+    dir_path: Path,
     drop_patient_if_outcome_before_date: Union[datetime, str],
     min_lookahead_days: int,
     pred_datetime_column: Optional[str] = "timestamp",
@@ -23,7 +24,7 @@ def load_dataset(
     Args:
         split_names (Union[list[str], str]): Names of splits, includes "train", "val",
             "test".
-        dir (Path): Directory of the dataset.
+        dir_path (Path): Directory of the dataset.
         drop_patient_if_outcome_before_date (Union[datetime, str]): Remove patients which
             experienced an outcome prior to the date. Also removes all visits prior to
             this date as otherwise the model might learn that no visits prior to the date can be tagged with the outcome.
@@ -61,7 +62,7 @@ def load_dataset(
             [
                 load_dataset(
                     split_names=split,
-                    dir=dir,
+                    dir_path=dir_path,
                     drop_patient_if_outcome_before_date=drop_patient_if_outcome_before_date,
                     min_lookahead_days=min_lookahead_days,
                     pred_datetime_column=pred_datetime_column,
@@ -75,7 +76,7 @@ def load_dataset(
     # Load dataset from csv
     dataset = load_dataset_from_dir(
         split_name=split_names,
-        dir=dir,
+        dir_path=dir_path,
         nrows=n_training_samples,
     )
 
@@ -128,7 +129,7 @@ def load_dataset(
 
 def load_dataset_from_dir(
     split_name: str,
-    dir: Path,
+    dir_path: Path,
     nrows: Optional[int],
 ) -> pd.DataFrame:
     """Load dataset from directory. Finds any .csv with the split name in its
@@ -136,7 +137,7 @@ def load_dataset_from_dir(
 
     Args:
         split_name (str): Name of split, allowed are ["train", "test", "val"]
-        dir (Path): Directory of the dataset.
+        dir_path (Path): Directory of the dataset.
         nrows (Optional[int]): Number of rows to load. Defaults to None, in which case
             all rows are loaded.
 
@@ -144,6 +145,6 @@ def load_dataset_from_dir(
         pd.DataFrame: The dataset
     """
     # Use glob to find the file
-    path = list(dir.glob(f"*{split_name}*.csv"))[0]
+    path = list(dir_path.glob(f"*{split_name}*.csv"))[0]
 
     return pd.read_csv(filepath_or_buffer=path, nrows=nrows)
diff --git a/src/psycopt2d/models.py b/src/psycopt2d/models.py
index b54af345..a5a7868e 100644
--- a/src/psycopt2d/models.py
+++ b/src/psycopt2d/models.py
@@ -1,3 +1,4 @@
+"""Specifications of models to be evaluated."""
 import numpy as np
 
 # from interpret.glassbox import ExplainableBoostingClassifier
@@ -6,13 +7,14 @@
 from xgboost import XGBClassifier
 
 
-def InitLogisticRegression(**kwargs):
+def init_logistic_regression(**kwargs):
+    """Initialize LogisticRegression model."""
     if "penalty_solver" in kwargs:
         kwargs["penalty"], kwargs["solver"] = kwargs.pop("penalty_solver").split("_")
     return LogisticRegression(**kwargs)
 
 
-logistic = {"model": InitLogisticRegression, "static_hyperparameters": {}}
+logistic = {"model": init_logistic_regression, "static_hyperparameters": {}}
 xgboost = {"model": XGBClassifier, "static_hyperparameters": {"missing": np.nan}}
 nb = {"model": GaussianNB, "static_hyperparameters": {}}
 
diff --git a/src/psycopt2d/synth_data_generator/synth_data_generator.py b/src/psycopt2d/synth_data_generator/synth_data_generator.py
index ae42ac45..defac04d 100644
--- a/src/psycopt2d/synth_data_generator/synth_data_generator.py
+++ b/src/psycopt2d/synth_data_generator/synth_data_generator.py
@@ -1,4 +1,10 @@
-# TODO: Refactor this to use only be an application of module in psycop-ml-utils instead.
+"""Refactor this to be an application of the module in psycop-ml-utils.
+
+Generator of synthetic data.
+"""
+
+# pylint: disable=too-many-locals,invalid-name,missing-function-docstring
+
 from pathlib import Path
 from typing import Optional, Union
 
@@ -12,11 +18,11 @@ def generate_synth_data(
     outcome_column_name: str,
     n_samples: int,
     logistic_outcome_model: str,
-    intercept: Optional[Union[int, float, complex, str, bytes]] = 0,
-    na_prob: Optional[float] = 0.01,
-    na_ignore_cols: list[str] = [],
-    prob_outcome: Optional[float] = 0.08,
-    noise_mean_sd: Optional[tuple[float, float]] = (0, 1),
+    intercept: Union[int, float, complex, str, bytes] = 0,
+    na_prob: float = 0.01,
+    na_ignore_cols: Optional[tuple[str]] = None,
+    prob_outcome: float = 0.08,
+    noise_mean_sd: tuple[float, float] = (0, 1),
 ) -> pd.DataFrame:
     """Takes a dict and generates synth data from it.
 
@@ -72,8 +78,9 @@ def generate_synth_data(
         df_ = df.mask(mask)
 
         # ignore nan values for non-nan columns.
-        for col in na_ignore_cols:
-            df_[col] = df[col]
+        if na_ignore_cols:
+            for col in na_ignore_cols:
+                df_[col] = df[col]
 
     # Sigmoid it to get probabilities with mean = 0.5
     df[outcome_column_name] = 1 / (1 + np.exp(y_))
diff --git a/src/psycopt2d/tables/performance_by_threshold.py b/src/psycopt2d/tables/performance_by_threshold.py
index 1f3cca26..30e4d51f 100644
--- a/src/psycopt2d/tables/performance_by_threshold.py
+++ b/src/psycopt2d/tables/performance_by_threshold.py
@@ -1,4 +1,6 @@
-from typing import Iterable, Optional, Union
+"""Get performance by which threshold is used to classify positive."""
+from collections.abc import Iterable
+from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -7,8 +9,8 @@
 
 
 def generate_performance_by_positive_rate_table(
-    labels: Iterable[Union[int, float]],
-    pred_probs: Iterable[Union[int, float]],
+    labels: Iterable[int],
+    pred_probs: Iterable[float],
     positive_rate_thresholds: Iterable[Union[int, float]],
     pred_proba_thresholds: Iterable[float],
     ids: Iterable[Union[int, float]],
@@ -20,8 +22,8 @@ def generate_performance_by_positive_rate_table(
     object.
 
     Args:
-        labels (Iterable[int, float]): True labels.
-        pred_probs (Iterable[int, float]): Predicted probabilities.
+        labels (Iterable[int]): True labels.
+        pred_probs (Iterable[float]): Predicted probabilities.
         positive_rate_thresholds (Iterable[float]): Positive_rate_thresholds to add to the table, e.g. 0.99, 0.98 etc.
             Calculated so that the Xth percentile of predictions are classified as the positive class.
         pred_proba_thresholds (Iterable[float]): Thresholds above which predictions are classified as positive.
@@ -48,7 +50,9 @@ def generate_performance_by_positive_rate_table(
             positive_threshold=threshold_value,
         )
 
-        threshold_metrics["total_warning_days"] = days_from_first_positive_to_diagnosis(
+        threshold_metrics[  # pylint: disable=unsupported-assignment-operation
+            "total_warning_days"
+        ] = days_from_first_positive_to_diagnosis(
             ids=ids,
             pred_probs=pred_probs,
             pred_timestamps=pred_timestamps,
@@ -57,7 +61,9 @@ def generate_performance_by_positive_rate_table(
             aggregation_method="sum",
         )
 
-        threshold_metrics["mean_warning_days"] = round(
+        threshold_metrics[  # pylint: disable=unsupported-assignment-operation
+            "mean_warning_days"
+        ] = round(
             days_from_first_positive_to_diagnosis(
                 ids=ids,
                 pred_probs=pred_probs,
@@ -87,7 +93,7 @@ def generate_performance_by_positive_rate_table(
         raise ValueError("Output format does not match anything that is allowed")
 
 
-def performance_by_threshold(
+def performance_by_threshold(  # pylint: disable=too-many-locals
     labels: Iterable[int],
     pred_probs: Iterable[float],
     positive_threshold: float,
@@ -107,30 +113,30 @@ def performance_by_threshold(
     """
     preds = np.where(pred_probs > positive_threshold, 1, 0)
 
-    CM = confusion_matrix(labels, preds)
+    conf_matrix = confusion_matrix(labels, preds)
 
-    TN = CM[0][0]
-    FN = CM[1][0]
-    TP = CM[1][1]
-    FP = CM[0][1]
+    true_neg = conf_matrix[0][0]
+    false_neg = conf_matrix[1][0]
+    true_pos = conf_matrix[1][1]
+    false_pos = conf_matrix[0][1]
 
-    n_total = TN + FN + TP + FP
+    n_total = true_neg + false_neg + true_pos + false_pos
 
-    true_prevalence = round((TP + FN) / n_total, round_to)
+    true_prevalence = round((true_pos + false_neg) / n_total, round_to)
 
-    positive_rate = round((TP + FP) / n_total, round_to)
-    negative_rate = round((TN + FN) / n_total, round_to)
+    positive_rate = round((true_pos + false_pos) / n_total, round_to)
+    negative_rate = round((true_neg + false_neg) / n_total, round_to)
 
-    PPV = round(TP / (TP + FP), round_to)
-    NPV = round(TN / (TN + FN), round_to)
+    pos_pred_val = round(true_pos / (true_pos + false_pos), round_to)
+    neg_pred_val = round(true_neg / (true_neg + false_neg), round_to)
 
-    Sensitivity = round(TP / (TP + FN), round_to)
-    Specificity = round(TN / (TN + FP), round_to)
+    sens = round(true_pos / (true_pos + false_neg), round_to)
+    spec = round(true_neg / (true_neg + false_pos), round_to)
 
-    FPR = round(FP / (TN + FP), round_to)
-    FNR = round(FN / (TP + FN), round_to)
+    false_pos_rate = round(false_pos / (true_neg + false_pos), round_to)
+    neg_pos_rate = round(false_neg / (true_pos + false_neg), round_to)
 
-    Accuracy = round((TP + TN) / n_total, round_to)
+    acc = round((true_pos + true_neg) / n_total, round_to)
 
     # Must return lists as values, otherwise pd.Dataframe requires setting indeces
     metrics_matrix = pd.DataFrame(
@@ -138,17 +144,17 @@ def performance_by_threshold(
             "positive_rate": [positive_rate],
             "negative_rate": [negative_rate],
             "true_prevalence": [true_prevalence],
-            "PPV": [PPV],
-            "NPV": [NPV],
-            "sensitivity": [Sensitivity],
-            "specificity": [Specificity],
-            "FPR": [FPR],
-            "FNR": [FNR],
-            "accuracy": [Accuracy],
-            "true_positives": [TP],
-            "true_negatives": [TN],
-            "false_positives": [FP],
-            "false_negatives": [FN],
+            "PPV": [pos_pred_val],
+            "NPV": [neg_pred_val],
+            "sensitivity": [sens],
+            "specificity": [spec],
+            "FPR": [false_pos_rate],
+            "FNR": [neg_pos_rate],
+            "accuracy": [acc],
+            "true_positives": [true_pos],
+            "true_negatives": [true_neg],
+            "false_positives": [false_pos],
+            "false_negatives": [false_neg],
         },
     )
 
diff --git a/src/psycopt2d/train_model.py b/src/psycopt2d/train_model.py
index d60bb630..1feea6ae 100644
--- a/src/psycopt2d/train_model.py
+++ b/src/psycopt2d/train_model.py
@@ -77,14 +77,14 @@ def load_dataset_from_config(cfg) -> tuple[pd.DataFrame, pd.DataFrame]:
 
         train = load_dataset(
             split_names="train",
-            dir=path,
+            dir_path=path,
             n_training_samples=cfg.data.n_training_samples,
             drop_patient_if_outcome_before_date=cfg.data.drop_patient_if_outcome_before_date,
             min_lookahead_days=cfg.data.min_lookahead_days,
         )
         val = load_dataset(
             split_names="val",
-            dir=path,
+            dir_path=path,
             n_training_samples=cfg.data.n_training_samples,
             drop_patient_if_outcome_before_date=cfg.data.drop_patient_if_outcome_before_date,
             min_lookahead_days=cfg.data.min_lookahead_days,
@@ -200,7 +200,7 @@ def main(cfg):
 
         print(
             f"Performance on train: {round(roc_auc_score(y_train, y_train_hat_prob), 3)}",
-        )  # TODO log to wandb
+        )  # ? log to wandb
 
         eval_dataset = val
         eval_dataset["y_hat_prob"] = y_val_hat_prob
diff --git a/src/psycopt2d/utils.py b/src/psycopt2d/utils.py
index eb6601f2..dfbe6a62 100644
--- a/src/psycopt2d/utils.py
+++ b/src/psycopt2d/utils.py
@@ -1,12 +1,16 @@
+"""Misc.
+
+utilities.
+"""
 import time
-from collections.abc import MutableMapping
+from collections.abc import Iterable, MutableMapping
 from pathlib import Path
-from typing import Any, Iterable, Union, dict, list
+from typing import Any, Union
 
 import dill as pkl
 import numpy as np
 import pandas as pd
-from omegaconf.dictconfig import dictConfig
+from omegaconf.dictconfig import DictConfig
 from wasabi import msg
 
 from psycopt2d.model_performance import ModelPerformance
@@ -183,13 +187,13 @@ def bin_continuous_data(series: pd.Series, bins: list[int]) -> pd.Series:
     8      51+
     """
     labels = []
-    for i, bin in enumerate(bins):
+    for i, bin_v in enumerate(bins):
         if i == 0:
-            labels.append(f"{bin}-{bins[i+1]}")
+            labels.append(f"{bin_v}-{bins[i+1]}")
         elif i < len(bins) - 2:
-            labels.append(f"{bin+1}-{bins[i+1]}")
+            labels.append(f"{bin_v+1}-{bins[i+1]}")
         elif i == len(bins) - 2:
-            labels.append(f"{bin+1}+")
+            labels.append(f"{bin_v+1}+")
         else:
             continue
 
@@ -247,13 +251,13 @@ def read_pickle(path: str) -> Any:
         return pkl.load(f)
 
 
-def prediction_df_with_metadata_to_disk(df: pd.DataFrame, cfg: dictConfig) -> None:
+def prediction_df_with_metadata_to_disk(df: pd.DataFrame, cfg: DictConfig) -> None:
     """Saves prediction dataframe with and hydra config to disk. Stored as a
     dict with keys "df" and "cfg".
 
     Args:
         df (pd.DataFrame): Dataframe to save.
-        cfg (dictConfig): Hydra config.
+        cfg (DictConfig): Hydra config.
     """
     model_args = format_dict_for_printing(cfg.model)
 
diff --git a/src/psycopt2d/visualization/__init__.py b/src/psycopt2d/visualization/__init__.py
index 69378691..d9d6b419 100644
--- a/src/psycopt2d/visualization/__init__.py
+++ b/src/psycopt2d/visualization/__init__.py
@@ -1,3 +1,4 @@
+"""Visualisations."""
 from .feature_importance import plot_feature_importances
 from .performance_over_time import (
     plot_auc_by_time_from_first_visit,
diff --git a/src/psycopt2d/visualization/altair_utils.py b/src/psycopt2d/visualization/altair_utils.py
index b99e7245..539f985b 100644
--- a/src/psycopt2d/visualization/altair_utils.py
+++ b/src/psycopt2d/visualization/altair_utils.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 from pathlib import Path
 from typing import Union
 
diff --git a/src/psycopt2d/visualization/base_charts.py b/src/psycopt2d/visualization/base_charts.py
index a9ed10d4..47adbccd 100644
--- a/src/psycopt2d/visualization/base_charts.py
+++ b/src/psycopt2d/visualization/base_charts.py
@@ -1,4 +1,6 @@
-from typing import Iterable, Optional
+"""Base charts."""
+from collections.abc import Iterable
+from typing import Optional
 
 import altair as alt
 import pandas as pd
diff --git a/src/psycopt2d/visualization/feature_importance.py b/src/psycopt2d/visualization/feature_importance.py
index 70ea625e..99156d66 100644
--- a/src/psycopt2d/visualization/feature_importance.py
+++ b/src/psycopt2d/visualization/feature_importance.py
@@ -1,4 +1,7 @@
-from typing import Iterable, Union, list
+"""Generate feature importances chart."""
+
+from collections.abc import Iterable
+from typing import Union
 
 import altair as alt
 import numpy as np
diff --git a/src/psycopt2d/visualization/performance_over_time.py b/src/psycopt2d/visualization/performance_over_time.py
index 16a3cbc2..89e4b060 100644
--- a/src/psycopt2d/visualization/performance_over_time.py
+++ b/src/psycopt2d/visualization/performance_over_time.py
@@ -3,7 +3,8 @@
 2. AUC by time from first visit
 3. AUC by time until diagnosis
 """
-from typing import Callable, Iterable, Optional, list
+from collections.abc import Callable, Iterable
+from typing import Optional
 
 import altair as alt
 import numpy as np
@@ -27,7 +28,7 @@ def _calc_performance(df: pd.DataFrame, metric: Callable) -> float:
     """
     if df.empty:
         return np.nan
-    elif metric == roc_auc_score and len(df["y"].unique()) == 1:
+    elif metric is roc_auc_score and len(df["y"].unique()) == 1:
         msg.info("Only 1 class present in bin. AUC undefined. Returning np.nan")
         return np.nan
     else:
@@ -105,7 +106,7 @@ def create_performance_by_time_from_event_df(
     prediction_timestamps: Iterable[pd.Timestamp],
     metric_fn: Callable,
     direction: str,
-    bins: list[int],
+    bins: Iterable[float],
     pretty_bins: Optional[bool] = True,
     drop_na_events: Optional[bool] = True,
 ) -> pd.DataFrame:
@@ -120,7 +121,7 @@ def create_performance_by_time_from_event_df(
         metric_fn (Callable): Which performance metric function to use (e.g. roc_auc_score)
         direction (str): Which direction to calculate time difference.
         Can either be 'prediction-event' or 'event-prediction'.
-        bins (list): Bins to group by.
+        bins (Iterable[float]): Bins to group by.
         pretty_bins (bool, optional): Whether to prettify bin names. I.e. make
             bins look like "1-7" instead of "[1-7)". Defaults to True.
         drop_na_events (bool, optional): Whether to drop rows where the event is NA. Defaults to True.
@@ -172,7 +173,7 @@ def plot_auc_by_time_from_first_visit(
     y_hat_probs: Iterable[int],
     first_visit_timestamps: Iterable[pd.Timestamp],
     prediction_timestamps: Iterable[pd.Timestamp],
-    bins=[0, 28, 182, 365, 730, 1825],
+    bins: tuple = (0, 28, 182, 365, 730, 1825),
     pretty_bins: Optional[bool] = True,
 ) -> alt.Chart:
     """Plot AUC as a function of time to first visit.
@@ -217,7 +218,7 @@ def plot_metric_by_time_until_diagnosis(
     y_hat: Iterable[int],
     diagnosis_timestamps: Iterable[pd.Timestamp],
     prediction_timestamps: Iterable[pd.Timestamp],
-    bins=[
+    bins: Iterable[int] = (
         -1825,
         -730,
         -365,
@@ -230,7 +231,7 @@ def plot_metric_by_time_until_diagnosis(
         365,
         730,
         1825,
-    ],
+    ),
     pretty_bins: Optional[bool] = True,
     metric_fn: Callable = f1_score,
     y_title: str = "F1",
diff --git a/src/psycopt2d/visualization/prob_over_time.py b/src/psycopt2d/visualization/prob_over_time.py
index 0f69e487..7481a497 100644
--- a/src/psycopt2d/visualization/prob_over_time.py
+++ b/src/psycopt2d/visualization/prob_over_time.py
@@ -1,7 +1,8 @@
 """Code for creating probabilities over time plots."""
 
+from collections.abc import Iterable
 from datetime import datetime
-from typing import Iterable, Optional, Union
+from typing import Optional, Union
 
 import altair as alt
 import pandas as pd
diff --git a/src/psycopt2d/visualization/sens_over_time.py b/src/psycopt2d/visualization/sens_over_time.py
index b5623b3e..4b5f5895 100644
--- a/src/psycopt2d/visualization/sens_over_time.py
+++ b/src/psycopt2d/visualization/sens_over_time.py
@@ -1,5 +1,6 @@
+"""Generate a plot of sensitivity by time to outcome."""
+from collections.abc import Iterable
 from functools import partial
-from typing import Iterable, list
 
 import altair as alt
 import numpy as np
@@ -14,7 +15,7 @@ def create_sensitivity_by_time_to_outcome_df(
     pred_proba_threshold: float,
     outcome_timestamps: Iterable[pd.Timestamp],
     prediction_timestamps: Iterable[pd.Timestamp],
-    bins=[0, 1, 7, 14, 28, 182, 365, 730, 1825],
+    bins: Iterable = (0, 1, 7, 14, 28, 182, 365, 730, 1825),
 ) -> pd.DataFrame:
     """Calculate sensitivity by time to outcome.
 
@@ -99,7 +100,7 @@ def plot_sensitivity_by_time_to_outcome(
     pred_proba_thresholds: list[float],
     outcome_timestamps: Iterable[pd.Timestamp],
     prediction_timestamps: Iterable[pd.Timestamp],
-    bins: list[int] = [0, 28, 182, 365, 730, 1825],
+    bins: Iterable[int] = (0, 28, 182, 365, 730, 1825),
 ):
     """Plot sensitivity by time to outcome.
 
diff --git a/tests/conftest.py b/tests/conftest.py
index cb836b2d..169b8907 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8,6 +8,7 @@
 
 @pytest.fixture
 def synth_data():
+    """Synthetic data."""
     df = pd.read_csv(Path("tests") / "test_data" / "synth_eval_data.csv")
     df = add_age_gender(df)
     return df
diff --git a/tests/test_auc_by_group_table.py b/tests/test_auc_by_group_table.py
index 0cccd349..b4103307 100644
--- a/tests/test_auc_by_group_table.py
+++ b/tests/test_auc_by_group_table.py
@@ -1,4 +1,5 @@
 """table_test_auc_by_group_table."""
+# pylint: disable=missing-function-docstring
 
 from psycopt2d.tables import auc_by_group_table
 from psycopt2d.utils import bin_continuous_data
diff --git a/tests/test_calculate_performance_metrics.py b/tests/test_calculate_performance_metrics.py
index 50be5f79..db630a4f 100644
--- a/tests/test_calculate_performance_metrics.py
+++ b/tests/test_calculate_performance_metrics.py
@@ -2,17 +2,17 @@
 # from psycopt2d.utils import calculate_performance_metrics
 
 
-def test_log_performance_metrics(synth_data):
-    pass
-    # # wandb.init(project="test")
-    # perf = calculate_performance_metrics(
-    #     synth_data,
-    #     outcome_col_name="label",
-    #     prediction_probabilities_col_name="pred_prob",
-    #     id_col_name="dw_ek_borger",
-    # )
-    # # stupid test - is actested in psycop-ml-utils
-    # # mainly used to test wandb but doesn't work GH actions
-    # assert type(perf) == dict
-    # # wandb.log(perf)
-    # # wandb.finish()
+# def test_log_performance_metrics(synth_data):
+#     pass
+# # wandb.init(project="test")
+# perf = calculate_performance_metrics(
+#     synth_data,
+#     outcome_col_name="label",
+#     prediction_probabilities_col_name="pred_prob",
+#     id_col_name="dw_ek_borger",
+# )
+# # stupid test - is actested in psycop-ml-utils
+# # mainly used to test wandb but doesn't work GH actions
+# assert type(perf) == dict
+# # wandb.log(perf)
+# # wandb.finish()
diff --git a/tests/test_performance_by_threshold.py b/tests/test_performance_by_threshold.py
index 111c2528..6d3b0630 100644
--- a/tests/test_performance_by_threshold.py
+++ b/tests/test_performance_by_threshold.py
@@ -1,3 +1,10 @@
+"""Generate performance by positive threshold.
+
+E.g. if predicted probability is .4, and threshold is .5, resolve to 0.
+"""
+
+# pylint: disable=missing-function-docstring
+
 from pathlib import Path
 
 import pandas as pd
@@ -12,6 +19,7 @@
 
 @pytest.fixture(scope="function")
 def synth_data():
+    """Load synthetic data."""
     csv_path = Path("tests") / "test_data" / "synth_eval_data.csv"
     df = pd.read_csv(csv_path)
 
@@ -32,7 +40,7 @@ def test_generate_performance_by_threshold_table(synth_data):
         positive_rate_thresholds=positive_rate_thresholds,
     )
 
-    t = generate_performance_by_positive_rate_table(
+    table = generate_performance_by_positive_rate_table(
         labels=df["label"],
         pred_probs=df["pred_prob"],
         ids=df["dw_ek_borger"],
@@ -66,8 +74,8 @@ def test_generate_performance_by_threshold_table(synth_data):
         },
     )
 
-    for col in t.columns:
-        t[col].equals(expected_df[col])
+    for col in table.columns:
+        table[col].equals(expected_df[col])
 
 
 def test_time_from_flag_to_diag(synth_data):
@@ -82,7 +90,7 @@ def test_time_from_flag_to_diag(synth_data):
         positive_rate_threshold=0.5,
     )
 
-    assert val > 290_000 and val < 292_000
+    assert 290_000 < val < 292_000
 
     # Threshold = 0.2
     val = days_from_first_positive_to_diagnosis(
@@ -93,4 +101,4 @@ def test_time_from_flag_to_diag(synth_data):
         positive_rate_threshold=0.2,
     )
 
-    assert val > 1_875_000 and val < 1_885_000
+    assert 1_875_000 < val < 1_885_000
diff --git a/tests/test_sens_over_time.py b/tests/test_sens_over_time.py
index 34761406..5ae3ede6 100644
--- a/tests/test_sens_over_time.py
+++ b/tests/test_sens_over_time.py
@@ -1,3 +1,5 @@
+"""Tests of sens over time."""
+# pylint: disable=missing-function-docstring
 from pathlib import Path
 
 import pandas as pd
@@ -20,24 +22,24 @@ def df():
     return df
 
 
-def test_plot_sensitivity_by_time_to_outcome(df):
-    # Disabled because of errors with altair. We're migrating away, re-enable when we're done.
+# def test_plot_sensitivity_by_time_to_outcome(df):
+# Disabled because of errors with altair. We're migrating away, re-enable when we're done.
 
-    # positive_rates = [0.95, 0.99, 0.999, 0.9999]
+# positive_rates = [0.95, 0.99, 0.999, 0.9999]
 
-    # pred_proba_thresholds = positive_rate_to_pred_probs(
-    #     pred_probs=df["pred_prob"],
-    #     positive_rate_thresholds=positive_rates,
-    # )
+# pred_proba_thresholds = positive_rate_to_pred_probs(
+#     pred_probs=df["pred_prob"],
+#     positive_rate_thresholds=positive_rates,
+# )
 
-    # plt = plot_sensitivity_by_time_to_outcome(
-    #     labels=df["label"],
-    #     y_hat_probs=df["pred_prob"],
-    #     pred_proba_thresholds=pred_proba_thresholds,
-    #     outcome_timestamps=df["timestamp_t2d_diag"],
-    #     prediction_timestamps=df["timestamp"],
-    #     bins=[0, 28, 182, 365, 730, 1825],
-    # )
+# plt = plot_sensitivity_by_time_to_outcome(
+#     labels=df["label"],
+#     y_hat_probs=df["pred_prob"],
+#     pred_proba_thresholds=pred_proba_thresholds,
+#     outcome_timestamps=df["timestamp_t2d_diag"],
+#     prediction_timestamps=df["timestamp"],
+#     bins=[0, 28, 182, 365, 730, 1825],
+# )
 
-    # plt.save("test_plot_sensitivity_by_time_to_outcome.png")
-    pass
+# plt.save("test_plot_sensitivity_by_time_to_outcome.png")
+# pass
diff --git a/tests/test_train_model.py b/tests/test_train_model.py
index 14a8fbe8..f30cc85f 100644
--- a/tests/test_train_model.py
+++ b/tests/test_train_model.py
@@ -1,3 +1,4 @@
+"""Test that the model trains correctly."""
 import platform
 
 import pytest
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 29fa10ed..b3ddf1fe 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,3 +1,5 @@
+"""Testing of the utils module."""
+# pylint: disable=missing-function-docstring
 import numpy as np
 import pandas as pd
 from utils_for_testing import str_to_df
diff --git a/tests/test_visualizations.py b/tests/test_visualizations.py
index 95abef3c..10ebd6a8 100644
--- a/tests/test_visualizations.py
+++ b/tests/test_visualizations.py
@@ -1,3 +1,8 @@
+"""Tests for all our visualisations.
+
+Mainly tests that they run without errors.
+"""
+# pylint: disable=missing-function-docstring
 from pathlib import Path
 
 import altair as alt
diff --git a/tests/utils_for_testing.py b/tests/utils_for_testing.py
index 6768dcad..dc75446a 100644
--- a/tests/utils_for_testing.py
+++ b/tests/utils_for_testing.py
@@ -1,11 +1,26 @@
+"""Misc.
+
+utils for testing.
+"""
 import numpy as np
 import pandas as pd
 
 
-def str_to_df(str, convert_timestamp_to_datetime: bool = True) -> pd.DataFrame:
+def str_to_df(string, convert_timestamp_to_datetime: bool = True) -> pd.DataFrame:
+    """Convert a string to a dataframe.
+
+    Args:
+        string (str): String to convert to a dataframe. String should be a csv.
+        convert_timestamp_to_datetime (bool, optional): Whether to convert
+            timestamp columns to datetime. Defaults to True.
+
+    Returns:
+        pd.DataFrame: The dataframe
+    """
+
     from io import StringIO
 
-    df = pd.read_table(StringIO(str), sep=",", index_col=False)
+    df = pd.read_table(StringIO(string), sep=",", index_col=False)
 
     if convert_timestamp_to_datetime:
         df = convert_cols_with_matching_colnames_to_datetime(df, "timestamp")
@@ -36,6 +51,12 @@ def convert_cols_with_matching_colnames_to_datetime(
 
 
 def add_age_gender(df):
+    """Add age and gender columns to dataframe.
+
+    Args:
+        df (pd.DataFrame): The dataframe to add age
+    """
+
     ids = pd.DataFrame({"dw_ek_borger": df["dw_ek_borger"].unique()})
     ids["age"] = np.random.randint(17, 95, len(ids))
     ids["gender"] = np.where(ids["dw_ek_borger"] > 30_000, "F", "M")

From 3e80894fc7365ab24c3e7bbe2baba4310c96fc40 Mon Sep 17 00:00:00 2001
From: Martin Bernstorff <martinbernstorff@gmail.com>
Date: Tue, 4 Oct 2022 14:10:45 +0200
Subject: [PATCH 76/77] ci: add python version to setup-python

---
 .github/workflows/pre-commit.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index fdf3492d..cecce73a 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -13,4 +13,6 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
     - uses: pre-commit/action@v3.0.0
\ No newline at end of file

From 5e9d61d60e30b18b278985c592a622b51b39c71d Mon Sep 17 00:00:00 2001
From: github-actions <action@github.com>
Date: Tue, 4 Oct 2022 12:51:42 +0000
Subject: [PATCH 77/77] 0.3.1

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 5 +++++
 pyproject.toml | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7ce858a6..57e1ed0d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,11 @@
 
 <!--next-version-placeholder-->
 
+## v0.3.1 (2022-10-04)
+### Fix
+* More linting, enable pylint pre-commit hook ([`03a0be1`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/03a0be1772737379cdcb2088934f6e7666d54013))
+* Some extra linting ([`de621e8`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/de621e8bbdb22addae980822f0926cfd733d1e3a))
+
 ## v0.3.0 (2022-10-03)
 ### Feature
 * Try decomposing actions ([`316e643`](https://github.com/Aarhus-Psychiatry-Research/psycop-t2d/commit/316e64335ee1b14aaf1c0a02fc7aad474af7a09a))
diff --git a/pyproject.toml b/pyproject.toml
index c135d610..7319bb72 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "psycopt2d"
-version = "0.3.0"
+version = "0.3.1"
 description = "Training scripts for the psycop-t2d project"
 authors = ["Your Name <you@example.com>"]