From 7ac8b734702843f26914d81909688de76a2e3c1a Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 08:42:49 -0700
Subject: [PATCH 1/9] Added bit to free up disk on linux, added a debug command
 to figure out what I need to clean on mac

---
 .github/workflows/CI.yaml | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index eb98e9f8..848aafc0 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -25,6 +25,41 @@ jobs:
         python-version: [3.9, "3.10", "3.11"]
 
     steps:
+      - name: Free diskspace (Linux)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo docker rmi $(docker image ls -aq) >/dev/null 2>&1 || true
+          sudo rm -rf \
+            /usr/share/dotnet /usr/local/lib/android /opt/ghc \
+            /usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \
+            /usr/lib/jvm || true
+          echo "some directories deleted"
+          sudo apt install aptitude -y >/dev/null 2>&1
+          sudo aptitude purge aria2 ansible azure-cli shellcheck rpm xorriso zsync \
+            esl-erlang firefox gfortran-8 gfortran-9 google-chrome-stable \
+            google-cloud-sdk imagemagick \
+            libmagickcore-dev libmagickwand-dev libmagic-dev ant ant-optional kubectl \
+            mercurial apt-transport-https mono-complete libmysqlclient \
+            unixodbc-dev yarn chrpath libssl-dev libxft-dev \
+            libfreetype6 libfreetype6-dev libfontconfig1 libfontconfig1-dev \
+            snmp pollinate libpq-dev postgresql-client powershell ruby-full \
+            sphinxsearch subversion mongodb-org azure-cli microsoft-edge-stable \
+            -y -f >/dev/null 2>&1
+          sudo aptitude purge google-cloud-sdk -f -y >/dev/null 2>&1
+          sudo aptitude purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
+          sudo apt purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
+          sudo aptitude purge '~n ^mysql' -f -y >/dev/null 2>&1
+          sudo aptitude purge '~n ^php' -f -y >/dev/null 2>&1
+          sudo aptitude purge '~n ^dotnet' -f -y >/dev/null 2>&1
+          sudo apt-get autoremove -y >/dev/null 2>&1
+          sudo apt-get autoclean -y >/dev/null 2>&1
+          echo "some packages purged"
+
+      - name: Free diskspace (MacOS)
+        if: matrix.os == 'macOS-latest'
+        run: |
+          sudo du -a * | sort -r -n | head -100
+
       - uses: actions/checkout@v3
 
       - name: Additional info about the build

From 2d3bb2e1fcd4f5de6a2abcf6d31d7922cacc3e0b Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 08:49:51 -0700
Subject: [PATCH 2/9] don't kill all jobs if one CI job fails

---
 .github/workflows/CI.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 848aafc0..3ccbf3db 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -20,6 +20,7 @@ jobs:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: [3.9, "3.10", "3.11"]

From 240c679f7d22256025a7596e9854d5d4571f5361 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 08:52:03 -0700
Subject: [PATCH 3/9] kill jobs if another push is made, also set the same
 shell for all steps

---
 .github/workflows/CI.yaml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 3ccbf3db..2554541c 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -15,6 +15,14 @@ on:
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * 0"
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
@@ -64,7 +72,6 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Additional info about the build
-        shell: bash
         run: |
           uname -a
           df -h
@@ -81,14 +88,12 @@ jobs:
 
       - name: Install package
         # conda setup requires this special shell
-        shell: bash -l {0}
         run: |
           python -m pip install . --no-deps
           micromamba list
 
       - name: Run tests
         # conda setup requires this special shell
-        shell: bash -l {0}
         run: |
           pytest -v --cov=modelforge --cov-report=xml --color=yes modelforge/tests/
 

From 47477501db2fd218ae66e34460262413460d0eda Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 08:59:22 -0700
Subject: [PATCH 4/9] more cleanup of env (defaults bad) and other CI tweaks

---
 .github/workflows/CI.yaml         | 8 ++++----
 devtools/conda-envs/test_env.yaml | 6 +-----
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 2554541c..c3ec59ff 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -78,12 +78,12 @@ jobs:
           ulimit -a
 
       # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
-      - uses: mamba-org/provision-with-micromamba@main
+      - uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: devtools/conda-envs/test_env.yaml
-          environment-name: test
-          channels: conda-forge,defaults
-          extra-specs: |
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
             python=${{ matrix.python-version }}
 
       - name: Install package
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 4ee2dd7c..240a1efd 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -1,8 +1,6 @@
 name: test
 channels:
   - conda-forge
-
-  - defaults
 dependencies:
   # Base depends
   - python
@@ -22,7 +20,7 @@ dependencies:
   - openff-units
   - pint
 
-    # Testing
+  # Testing
   - pytest
   - pytest-cov
   - codecov
@@ -30,7 +28,5 @@ dependencies:
   - qcportal
   - requests
 
-    # Pip-only installs
   - pip:
       - pedantic
-  #  - codecov

From 38722ef25972a602244897bcb13c3814bf9ccd1b Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 09:06:34 -0700
Subject: [PATCH 5/9] fix syntax mistake in du command

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

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index c3ec59ff..eda5a5d4 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -67,7 +67,7 @@ jobs:
       - name: Free diskspace (MacOS)
         if: matrix.os == 'macOS-latest'
         run: |
-          sudo du -a * | sort -r -n | head -100
+          sudo du -a / | sort -r -n | head -100
 
       - uses: actions/checkout@v3
 

From f05584e14e91b3ac5fb70d92315f08d260ecaf72 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 11:18:41 -0700
Subject: [PATCH 6/9] pin problematic package

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 240a1efd..10b7bd90 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -14,7 +14,7 @@ dependencies:
   - loguru
   - gdown
   - tqdm
-  - lightning
+  - lightning=2.0.8
   - tensorboard
   - torchvision
   - openff-units

From 409623f2a891c47b1c5fd5021014d175133e0dfb Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 11:19:26 -0700
Subject: [PATCH 7/9] test if xdist speeds things up

---
 .github/workflows/CI.yaml         | 37 +------------------------------
 devtools/conda-envs/test_env.yaml |  1 +
 2 files changed, 2 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index eda5a5d4..f799e3e2 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -34,41 +34,6 @@ jobs:
         python-version: [3.9, "3.10", "3.11"]
 
     steps:
-      - name: Free diskspace (Linux)
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          sudo docker rmi $(docker image ls -aq) >/dev/null 2>&1 || true
-          sudo rm -rf \
-            /usr/share/dotnet /usr/local/lib/android /opt/ghc \
-            /usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \
-            /usr/lib/jvm || true
-          echo "some directories deleted"
-          sudo apt install aptitude -y >/dev/null 2>&1
-          sudo aptitude purge aria2 ansible azure-cli shellcheck rpm xorriso zsync \
-            esl-erlang firefox gfortran-8 gfortran-9 google-chrome-stable \
-            google-cloud-sdk imagemagick \
-            libmagickcore-dev libmagickwand-dev libmagic-dev ant ant-optional kubectl \
-            mercurial apt-transport-https mono-complete libmysqlclient \
-            unixodbc-dev yarn chrpath libssl-dev libxft-dev \
-            libfreetype6 libfreetype6-dev libfontconfig1 libfontconfig1-dev \
-            snmp pollinate libpq-dev postgresql-client powershell ruby-full \
-            sphinxsearch subversion mongodb-org azure-cli microsoft-edge-stable \
-            -y -f >/dev/null 2>&1
-          sudo aptitude purge google-cloud-sdk -f -y >/dev/null 2>&1
-          sudo aptitude purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
-          sudo apt purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
-          sudo aptitude purge '~n ^mysql' -f -y >/dev/null 2>&1
-          sudo aptitude purge '~n ^php' -f -y >/dev/null 2>&1
-          sudo aptitude purge '~n ^dotnet' -f -y >/dev/null 2>&1
-          sudo apt-get autoremove -y >/dev/null 2>&1
-          sudo apt-get autoclean -y >/dev/null 2>&1
-          echo "some packages purged"
-
-      - name: Free diskspace (MacOS)
-        if: matrix.os == 'macOS-latest'
-        run: |
-          sudo du -a / | sort -r -n | head -100
-
       - uses: actions/checkout@v3
 
       - name: Additional info about the build
@@ -95,7 +60,7 @@ jobs:
       - name: Run tests
         # conda setup requires this special shell
         run: |
-          pytest -v --cov=modelforge --cov-report=xml --color=yes modelforge/tests/
+          pytest -v -n auto --cov=modelforge --cov-report=xml --color=yes modelforge/tests/
 
       - name: CodeCov
         uses: codecov/codecov-action@v3
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 10b7bd90..58ebd08a 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -23,6 +23,7 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
+  - pytest-xdist
   - codecov
   - qcelemental=0.25.1
   - qcportal

From b37aff8ac75957035393e4e29a3243078f23a658 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 11:30:29 -0700
Subject: [PATCH 8/9] looks like xdist breaks some tests

---
 .github/workflows/CI.yaml         | 2 +-
 devtools/conda-envs/test_env.yaml | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index f799e3e2..a387d7b3 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -60,7 +60,7 @@ jobs:
       - name: Run tests
         # conda setup requires this special shell
         run: |
-          pytest -v -n auto --cov=modelforge --cov-report=xml --color=yes modelforge/tests/
+          pytest -v --cov=modelforge --cov-report=xml --color=yes modelforge/tests/
 
       - name: CodeCov
         uses: codecov/codecov-action@v3
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 58ebd08a..10b7bd90 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -23,7 +23,6 @@ dependencies:
   # Testing
   - pytest
   - pytest-cov
-  - pytest-xdist
   - codecov
   - qcelemental=0.25.1
   - qcportal

From 9f5a6f9a678609d1b5394b210d8c5d6a485cb596 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 15 Sep 2023 12:09:09 -0700
Subject: [PATCH 9/9] print 10 slowest tests

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

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index a387d7b3..70df4f58 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -60,7 +60,7 @@ jobs:
       - name: Run tests
         # conda setup requires this special shell
         run: |
-          pytest -v --cov=modelforge --cov-report=xml --color=yes modelforge/tests/
+          pytest -v --cov=modelforge --cov-report=xml --color=yes --durations=10 modelforge/tests/
 
       - name: CodeCov
         uses: codecov/codecov-action@v3