From c4751b7107582789fcb81b890231b30df919364f Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 12:57:13 +0100 Subject: [PATCH 01/17] Add badges --- README.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/README.md b/README.md index 0d913ce7e..d013f93be 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,18 @@ +
+
+ +[![ci](https://github.com/emdgroup/BayBE/actions/workflows/ci.yml/badge.svg)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Aci.yml) +[![regular](https://github.com/emdgroup/BayBE/actions/workflows/regular.yml/badge.svg)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Aregular.yml) + +Conda Version + + + + + +

Documentation

+
+ # BayBE โ€” A Bayesian Back End for Design of Experiments This software package provides a general-purpose toolbox for **Design of Experiments From 3ddd452d221c550f38a020c076aeb2569b504280 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 12:57:42 +0100 Subject: [PATCH 02/17] Remove caution note --- README.md | 9 --------- 1 file changed, 9 deletions(-) diff --git a/README.md b/README.md index d013f93be..335cdf3c2 100644 --- a/README.md +++ b/README.md @@ -27,15 +27,6 @@ It provides the necessary functionality to: - handle measurements data and feed it back into the experimental design. - compare different DOE strategies through backtesting with synthetic and real data. -## โ—๐Ÿšง This repository is under **heavy active development**. ๐Ÿšงโ— - -Please note that the provided functionality and user interfaces are not stable and may -change in newer releases. -Therefore, if you would like to use the code in its current early stage, we recommend -pinning the version during installation to prevent possible changes in the backend. -In case of questions or comments, feel free to reach out to the **BayBE Dev Team** (see -[the contributors page](docs/misc/contributors_link) for contact details). - ## Installation There are several ways to install BayBE. From 54e82e42c7335798e5ec4860c881837b3f3e2a82 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 13:06:09 +0100 Subject: [PATCH 03/17] Rework installation section --- README.md | 37 ++++++++----------------------------- 1 file changed, 8 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index 335cdf3c2..b356ed62c 100644 --- a/README.md +++ b/README.md @@ -28,40 +28,18 @@ It provides the necessary functionality to: - compare different DOE strategies through backtesting with synthetic and real data. ## Installation - -There are several ways to install BayBE. -Essentially, these can be divided into 1) installation from Azure Artifacts via pip -or 2) direct installation from this repository using git. - -### Installation from Azure Artifacts - -If a specific **released** BayBE version is to be installed, this can be achieved via -[Azure Artifacts](https://***REMOVED***/_artifacts/feed/artifacts). - -The most convenient way for this is to generate a personal access token (PAT) on the -[user settings page](https://***REMOVED***/_usersSettings/tokens). -Once the token is created, BayBE can be installed via +### From Package Index +The easiest way to install BayBE is via PyPI or Conda: ```bash -pip install --extra-index-url https://artifacts:@pkgs.***REMOVED***/_packaging/artifacts/pypi/simple/ baybe +pip install baybe ``` -where `` needs to be replaced with your PAT. -Note that, instead of passing the `--extra-index-url` option directly as an argument -to the `install` command, you can alternatively create a `pip.conf` file containing -the same information. - -A second way to authenticate instead of using a PAT is via `artifacts-keyring`. -To do so, ensure that all [prerequisites](https://pypi.org/project/artifacts-keyring/) -are fulfilled and run: - ```bash -pip install keyring artifacts-keyring -pip install --extra-index-url https://pkgs.***REMOVED***/_packaging/artifacts/pypi/simple/ baybe +conda install --channel=conda-forge baybe ``` ### Installation from Repository - If you need finer control and would like to install a specific commit that has not been released under a certain version tag, you can do so by installing BayBE directly from the repository. @@ -73,8 +51,9 @@ pip install . ``` There are additional dependencies that can be installed corresponding to linters, -plotters etc. (`dev`). A developer would typically also install the package in editable mode -('-e'). +formatters etc. (e.g. `dev`). A developer would typically also install the package in +editable mode ('-e') which ensures that changes to the code do not require a +reinstallation. ```bash pip install -e '.[dev]' @@ -99,7 +78,7 @@ The available groups are: - `onnx`: Required for using custom surrogate models in ONNX format. - `simulation`: Enabling the [`simulation`](baybe.simulation) module. - `test`: Required for running the tests. -- `dev`: All of the above plus `tox` and `pip-audit`. +- `dev`: All of the above plus `tox` and `pip-audit`. For code contributors. ## Getting Started From 79d8f3f39f41ac24145fd6fda779d31b7ba2b038 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 14:37:47 +0100 Subject: [PATCH 04/17] Move telemetry README content --- README.md | 49 ---------------------------------- baybe/telemetry.py | 66 ++++++++++++++++++++++++++++++++++++++++------ 2 files changed, 58 insertions(+), 57 deletions(-) diff --git a/README.md b/README.md index b356ed62c..acd79f2a8 100644 --- a/README.md +++ b/README.md @@ -296,55 +296,6 @@ campaign.add_measurements(df) With the newly arrived data, BayBE will update its internal state and can produce a refined design for the next iteration. -## Telemetry - -By default, BayBE collects anonymous usage statistics. -Note that this does **not** involve logging of recorded measurements, targets or any -project information that would allow the reconstruction of details. - -Monitored quantities are: - -- `batch_quantity` used when querying recommendations -- number of parameters in the search space -- number of constraints in the search space -- how often `recommend` was called -- how often `add_measurements` was called -- how often a search space is newly created -- how often initial measurements are added before recommendations were calculated - ("naked initial measurements") -- the fraction of measurements added that correspond to previous recommendations - -These metrics are vital to demonstrating the impact of the project and -โ€“ should you find BayBE useful โ€“ we kindly ask you to leave telemetry activated. -If you wish to disable logging, you can set the following environment variable: - -```bash -export BAYBE_TELEMETRY_ENABLED=false -``` - -or in python: - -```python -import os - -os.environ["BAYBE_TELEMETRY_ENABLED"] = "false" -``` - -before calling any BayBE functionality. -Telemetry can be re-enabled by simply removing the variable: - -```bash -unset BAYBE_TELEMETRY_ENABLED -``` - -or in python: - -```python -os.environ.pop["BAYBE_TELEMETRY_ENABLED"] -``` - -Note, however, that (un-)setting the variable in the shell will not affect the running -Python session. ## Known Issues A list of know issues can be found [here](docs/known_issues.md). diff --git a/baybe/telemetry.py b/baybe/telemetry.py index 7b0f27b50..a569f8ef0 100644 --- a/baybe/telemetry.py +++ b/baybe/telemetry.py @@ -1,27 +1,77 @@ """Telemetry functionality for BayBE. -The following environment variables control the behavior of BayBE telemetry: - -BAYBE_TELEMETRY_ENABLED +Important: + BayBE collects anonymous usage statistics **only** for employees of Merck KGaA, + Darmstadt, Germany and/or its affiliates. The recording of metrics is turned off + for all other users and impossible due to a VPN block. In any case, the usage + statistics do **not** involve logging of recorded measurements, targets or any + project information that would allow for reconstruction of details. The user and + host machine names are irreversibly anonymized. + +**Monitored quantities are:** + * ``batch_quantity`` used when querying recommendations + * Number of parameters in the search space + * Number of constraints in the search space + * How often ``recommend`` was called + * How often ``add_measurements`` was called + * How often a search space is newly created + * How often initial measurements are added before recommendations were calculated + ("naked initial measurements") + * The fraction of measurements added that correspond to previous recommendations + * Each measurement is associated with an irreversible has of the user- and hostname + +**The following environment variables control the behavior of BayBE telemetry:** + +``BAYBE_TELEMETRY_ENABLED`` Flag that can turn off telemetry entirely (default is `true`). To turn it off set it to `false`. -BAYBE_TELEMETRY_ENDPOINT +``BAYBE_TELEMETRY_ENDPOINT`` The receiving endpoint URL for telemetry data. -BAYBE_TELEMETRY_VPN_CHECK +``BAYBE_TELEMETRY_VPN_CHECK`` Flag turning an initial telemetry connectivity check on/off (default is `true`). -BAYBE_TELEMETRY_VPN_CHECK_TIMEOUT +``BAYBE_TELEMETRY_VPN_CHECK_TIMEOUT`` The timeout in seconds for the check whether the endpoint URL is reachable. -BAYBE_TELEMETRY_USERNAME +``BAYBE_TELEMETRY_USERNAME`` The name of the user executing BayBE code. Defaults to an irreversible hash of the username according to the OS. -BAYBE_TELEMETRY_HOSTNAME +``BAYBE_TELEMETRY_HOSTNAME`` The name of the machine executing BayBE code. Defaults to an irreversible hash of the machine name. + +If you wish to disable logging, you can set the following environment variable: + +.. code-block:: terminal + + export BAYBE_TELEMETRY_ENABLED=false + +or in Python: + +.. code-block:: python + + import os + os.environ["BAYBE_TELEMETRY_ENABLED"] = "false" + +before calling any BayBE functionality. + +Telemetry can be re-enabled by simply removing the variable: + +.. code-block:: terminal + + unset BAYBE_TELEMETRY_ENABLED + +or in Python: + +.. code-block:: python + + os.environ.pop["BAYBE_TELEMETRY_ENABLED"] + +Note, however, that (un-)setting the variable in the shell will not affect the running +Python session. """ import getpass import hashlib From 338311cc499650ba9fea43a48be6bd7cc6efb950 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 15:15:44 +0100 Subject: [PATCH 05/17] Add images --- README.md | 5 + docs/images/banner1.svg | 259 ++++++++++++++++++++++++++++ docs/images/banner2.svg | 257 ++++++++++++++++++++++++++++ docs/images/logo1.svg | 366 ++++++++++++++++++++++++++++++++++++++++ docs/images/logo2.svg | 362 +++++++++++++++++++++++++++++++++++++++ 5 files changed, 1249 insertions(+) create mode 100644 docs/images/banner1.svg create mode 100644 docs/images/banner2.svg create mode 100644 docs/images/logo1.svg create mode 100644 docs/images/logo2.svg diff --git a/README.md b/README.md index acd79f2a8..cf0798004 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,8 @@ +[![Logo](https://raw.githubusercontent.com/emdgroup/baybe/main/docs/images/banner2.svg)](https://github.com/emdgroup/baybe) +

Documentation

@@ -296,6 +298,9 @@ campaign.add_measurements(df) With the newly arrived data, BayBE will update its internal state and can produce a refined design for the next iteration. +## Telemetry + + ## Known Issues A list of know issues can be found [here](docs/known_issues.md). diff --git a/docs/images/banner1.svg b/docs/images/banner1.svg new file mode 100644 index 000000000..472068a9d --- /dev/null +++ b/docs/images/banner1.svg @@ -0,0 +1,259 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bayesian + + + Back End + + + BE + + + B + + + ay + + + diff --git a/docs/images/banner2.svg b/docs/images/banner2.svg new file mode 100644 index 000000000..ab0705b09 --- /dev/null +++ b/docs/images/banner2.svg @@ -0,0 +1,257 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bayesian + + + Back End + + + BE + + + B + + + ay + + + diff --git a/docs/images/logo1.svg b/docs/images/logo1.svg new file mode 100644 index 000000000..d6ff7d027 --- /dev/null +++ b/docs/images/logo1.svg @@ -0,0 +1,366 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bayesian + Back + End + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/images/logo2.svg b/docs/images/logo2.svg new file mode 100644 index 000000000..535ae6721 --- /dev/null +++ b/docs/images/logo2.svg @@ -0,0 +1,362 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bayesian + Back + End + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From aab5654a028b92daf50089ff7f443311f374e7ce Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 15:16:44 +0100 Subject: [PATCH 06/17] Update CHANGELOG.md --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d66b6193c..fe0130675 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Github CI pipelines - Optional --force option for force building the documentation despite errors - Enabled passing optional arguments to `tox -e docs` calls +- Logo and banner images + +### +- reworked README ### Changed - Now has concise contribution guidelines From 20ce6f6c00dda1b1db4b5d9cd42b140245d3d647 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 15:45:53 +0100 Subject: [PATCH 07/17] Edit intro text --- README.md | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index cf0798004..b28aa5f7a 100644 --- a/README.md +++ b/README.md @@ -17,17 +17,19 @@ # BayBE โ€” A Bayesian Back End for Design of Experiments -This software package provides a general-purpose toolbox for **Design of Experiments -(DOE)**. - -It provides the necessary functionality to: - -- manage experimental design spaces that can be defined through various types of - experimental parameters. -- execute different kinds of DOE strategies, levering both classical and - machine-learning-based models. -- handle measurements data and feed it back into the experimental design. -- compare different DOE strategies through backtesting with synthetic and real data. +The **Bay**esian **B**ack **E**nd provides a general-purpose toolbox for Bayesian Design of +Experiments, focusing on additions that enable real-world experimental campaigns. + +Besides functionality to perform a typical recommend-measure loop, BayBE's highlights are: +- Custom parameter encodings: Improve your campaign with domain knowledge +- Built-in chemical encodings: Improve your campaign with chemical knowledge +- Single and multiple targets with min, max and match objectives +- Custom surrogate models: For specialized problems or active learning +- Hybrid (mixed continuous and discrete) spaces +- Transfer learning: Mix data from multiple campaigns and accelerate optimization +- Comprehensive backtest, simulation and imputation utilities: Benchmark and find your best settings +- Fully typed and hypothesis-tested: Robust code base +- The entire state of your campaign is fully de-/serializable: Useful for storing results in databases ## Installation ### From Package Index @@ -41,7 +43,7 @@ pip install baybe conda install --channel=conda-forge baybe ``` -### Installation from Repository +### From Repository If you need finer control and would like to install a specific commit that has not been released under a certain version tag, you can do so by installing BayBE directly from the repository. @@ -298,9 +300,6 @@ campaign.add_measurements(df) With the newly arrived data, BayBE will update its internal state and can produce a refined design for the next iteration. -## Telemetry - - ## Known Issues A list of know issues can be found [here](docs/known_issues.md). From 63e34865a56e6b366f9d9148eb898f3ad7ec55ba Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 17:26:34 +0100 Subject: [PATCH 08/17] Add typo exception --- README.md | 4 ++-- _typos.toml | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 _typos.toml diff --git a/README.md b/README.md index b28aa5f7a..044622f59 100644 --- a/README.md +++ b/README.md @@ -85,14 +85,14 @@ The available groups are: - `dev`: All of the above plus `tox` and `pip-audit`. For code contributors. -## Getting Started +## Quick Start BayBE is a DOE software built to streamline your experimental process. It can process measurement data from previous experiments and, based on these, provide optimal experimental designs to further improve your target quantities. In order to make use of BayBE's optimization capabilities, you need to translate your -real-world optimization problem into mathematical language. +real-world problem into mathematical language. To do so, you should ask yourself the following questions: * What should be optimized? diff --git a/_typos.toml b/_typos.toml new file mode 100644 index 000000000..359d0fd56 --- /dev/null +++ b/_typos.toml @@ -0,0 +1,2 @@ +[type.md] +extend-ignore-identifiers-re = ['^E*nd$'] # ignore `**E**nd` in README.md \ No newline at end of file From 0e18b062c8e3c18693a9821e9c15d7d044a947f5 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 17:36:44 +0100 Subject: [PATCH 09/17] Delete Azure pipeline --- azure-pipelines.yml | 261 -------------------------------------------- 1 file changed, 261 deletions(-) delete mode 100644 azure-pipelines.yml diff --git a/azure-pipelines.yml b/azure-pipelines.yml deleted file mode 100644 index f620a48ef..000000000 --- a/azure-pipelines.yml +++ /dev/null @@ -1,261 +0,0 @@ -# Formatting, linting, testing, and code release - -trigger: - branches: - include: - - main - - refs/tags/* - -variables: - coverage_overall_threshold: 70 - coverage_individual_threshold: 45 - -stages: - -- stage: Lint - displayName: "Format, Lint, Asserts" - - jobs: - - job: "Lint" - - pool: - vmImage: ubuntu-20.04 - - strategy: - matrix: - Py3.8: - python.version: '3.8.x' - tox.env: 'py38' - Py3.9: - python.version: '3.9.x' - tox.env: 'py39' - Py3.10: - python.version: '3.10.x' - tox.env: 'py310' - Py3.11: - python.version: '3.11.x' - tox.env: 'py311' - - steps: - - checkout: self - - - task: UsePythonVersion@0 - inputs: - versionSpec: '$(python.version)' - displayName: 'Use Python $(python.version)' - - - script: | - pip install tox - tox -e lint - displayName: "Pre-commit linter/formatter stack" - - - job: "Audit" - - pool: - vmImage: ubuntu-20.04 - - strategy: - matrix: - Py3.8: - python.version: '3.8.x' - tox.env: 'py38' - Py3.9: - python.version: '3.9.x' - tox.env: 'py39' - Py3.10: - python.version: '3.10.x' - tox.env: 'py310' - Py3.11: - python.version: '3.11.x' - tox.env: 'py311' - - steps: - - checkout: self - - - task: UsePythonVersion@0 - inputs: - versionSpec: '$(python.version)' - displayName: 'Use Python $(python.version)' - - - script: | - pip install tox - tox -e audit - displayName: "Pip-audit" - - - job: "Changelog" - condition: | - and( - ne(variables['Build.SourceBranch'], 'refs/heads/main'), - not(startsWith(variables['build.sourceBranch'], 'refs/tags/')) - ) - pool: - vmImage: ubuntu-20.04 - - steps: - - script: | - NUM_ADDED=`git diff --numstat origin/main HEAD CHANGELOG.md | cut -d$'\t' -f1` - echo "Changelog differences: $NUM_ADDED" - if [ "$NUM_ADDED" -gt "0" ]; then - echo "SUCCESS" - exit 0 - else - echo "ERROR - Nothing has been added to CHANGELOG.md" - exit 1 - fi - displayName: "Assert Changelog Edit" - - -- stage: Unit_Tests - displayName: "Unit Tests" - - jobs: - - job: "PyTest_full" - displayName: "Pytest (full)" - pool: - vmImage: ubuntu-20.04 - - strategy: - matrix: - Py3.8: - python.version: '3.8.x' - tox.env: 'py38' - Py3.9: - python.version: '3.9.x' - tox.env: 'py39' - Py3.10: - python.version: '3.10.x' - tox.env: 'py310' - Py3.11: - python.version: '3.11.x' - tox.env: 'py311' - - steps: - - checkout: self - - - task: UsePythonVersion@0 - inputs: - versionSpec: '$(python.version)' - displayName: 'Use Python $(python.version)' - - - script: | - pip install tox unittest-xml-reporting pytest-azurepipelines - tox -e fulltest-$(tox.env) -- --cov-report=xml --junit-xml $(System.DefaultWorkingDirectory)/junit.xml - displayName: "PyTest" - - # Fail if overall coverage is too low - - script: | - pip install coverage - coverage report --fail-under=$(coverage_overall_threshold) - displayName: "Assert Overall Coverage" - - # Fail if any individual coverage is too low - - script: | - pip install coverage - coverage report | - grep -E -o '[0-9]+%' | - tr -d '%' | - sed '$d' | - awk '{if ($1<$(coverage_individual_threshold)) exit 1 }' - displayName: "Assert Individual Coverage" - - # Publish code coverage for Python38 - - task: PublishCodeCoverageResults@1 - condition: eq(variables['tox.env'], 'py38') - displayName: "Publish Coverage Report" - inputs: - codeCoverageTool: Cobertura - summaryFileLocation: $(System.DefaultWorkingDirectory)/coverage.xml - #reportDirectory: $(System.DefaultWorkingDirectory)/**/htmlcov - - - task: PublishTestResults@2 - condition: eq(variables['tox.env'], 'py38') - displayName: "Publish Test Results" - inputs: - testResultsFiles: $(System.DefaultWorkingDirectory)/junit.xml - #testRunTitle: 'Rest results for Python $(python.version)' - - - job: "PyTest_Core" - displayName: "Pytest (core)" - pool: - vmImage: ubuntu-20.04 - - strategy: - matrix: - Py3.8: - python.version: '3.8.x' - tox.env: 'py38' - Py3.9: - python.version: '3.9.x' - tox.env: 'py39' - Py3.10: - python.version: '3.10.x' - tox.env: 'py310' - Py3.11: - python.version: '3.11.x' - tox.env: 'py311' - - steps: - - checkout: self - - - task: UsePythonVersion@0 - inputs: - versionSpec: '$(python.version)' - displayName: 'Use Python $(python.version)' - - - script: | - pip install tox unittest-xml-reporting pytest-azurepipelines - tox -e coretest-$(tox.env) -- --cov-report=xml --junit-xml $(System.DefaultWorkingDirectory)/junit.xml - displayName: "PyTest" - - -- stage: Release # taken from foundry-local - displayName: "Publish package" - condition: startsWith(variables['build.sourceBranch'], 'refs/tags/') - jobs: - - job: "Release" - - pool: - vmImage: ubuntu-20.04 - - steps: - - task: PipAuthenticate@1 - inputs: - artifactFeeds: "artifacts" # Reactivate once upstream is up to date - # Setting this variable to "true" will force pip to get distributions from official python registry first and fallback to feeds mentioned above if distributions are not found there. - onlyAddExtraIndex: true - displayName: "Pip Authenticate" - - - script: | - pip wheel . --no-deps --wheel-dir dist - ls -lat dist - displayName: "Create Wheel" - - - script: | - WHL_PATH=$( find dist -name "*.whl") - echo $WHL_PATH - echo "##vso[task.setvariable variable=whlName]$WHL_PATH" - displayName: "Get whl Filename" - - - publish: $(System.DefaultWorkingDirectory)/$(whlName) - artifact: baybe_pipeline_snapshot - displayName: "Upload Snapshot Artifact" - - # publish on tagged build - - script: | - pip install twine - condition: startsWith(variables['build.sourceBranch'], 'refs/tags/') - displayName: "Install Twine" - - - task: TwineAuthenticate@1 - inputs: - artifactFeed: artifacts - condition: startsWith(variables['build.sourceBranch'], 'refs/tags/') - displayName: "Twine Authenticate" - - # https://docs.microsoft.com/en-us/azure/devops/pipelines/artifacts/pypi?view=azure-devops&tabs=yaml - - script: | - echo Uploading $(whlName) - cat $(PYPIRC_PATH) - twine upload -r artifacts --config-file $(PYPIRC_PATH) --verbose $(whlName) - condition: startsWith(variables['build.sourceBranch'], 'refs/tags/') - displayName: "Twine Upload" \ No newline at end of file From 1e3e5acc1596af819416dbb97140f1f8e3baeb0a Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Tue, 28 Nov 2023 18:24:38 +0100 Subject: [PATCH 10/17] Compress quick start part of README.md --- README.md | 152 ++++++++++++++++-------------------------------------- 1 file changed, 45 insertions(+), 107 deletions(-) diff --git a/README.md b/README.md index 044622f59..e8173574d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,11 @@ [![Logo](https://raw.githubusercontent.com/emdgroup/baybe/main/docs/images/banner2.svg)](https://github.com/emdgroup/baybe) -

Documentation

+Documentation + โ€ข  +User Guide + โ€ข  +Contribute # BayBE โ€” A Bayesian Back End for Design of Experiments @@ -87,85 +91,38 @@ The available groups are: ## Quick Start -BayBE is a DOE software built to streamline your experimental process. -It can process measurement data from previous experiments and, based on these, provide -optimal experimental designs to further improve your target quantities. - -In order to make use of BayBE's optimization capabilities, you need to translate your -real-world problem into mathematical language. -To do so, you should ask yourself the following questions: - -* What should be optimized? -* What are the degrees of freedom? -* (Optional) What optimization strategy should be used? - -Conveniently, the answer to each of these questions can be directly expressed in the -form of objects in BayBE's ecosystem that can be easily mixed and matched: - -| Part of the Problem Specification | Defining BayBE Objects | -|:------------------------------------------------------|:--------------------------| -| What should be optimized? | `Objective`, `Target` | -| What are the degrees of freedom? | `Parameter`, `Constraint` | -| (Optional) What optimization strategy should be used? | `Strategy`, `Recommender` | - -The objects in the first two table rows can be regarded as embodiments of the -**mathematical DOE specifications** in digital form, as they fully define the underlying -optimization problem. -By contrast, the objects in the last row rather provide **algorithmic details** -on how the DOE problem should be solved. -In that sense, the former carry information that **must be** provided by the user, -whereas the latter are **optional** settings that can also be set automatically -by BayBE. - -A key element in the design of BayBE is the [`Campaign`](baybe.campaign.Campaign) object. -It acts as a central container for all the necessary information and objects -associated with an experimentation process, ensuring that all independent model -components (e.g. the objective function, the search space, etc.) are properly combined. - -The following example provides a step-by-step guide to what this translation process -should look like, and how we can subsequently use BayBE to generate optimal sets of -experimental conditions. +Let us consider a simple experiment where we have three parameters and want to maximize +a single target called `Yield`. ### Defining the Optimization Objective -We start by defining an optimization objective. -While BayBE ships with the necessary functionality to optimize multiple targets -simultaneously, as an introductory example, we consider a simple scenario where our -goal is to **maximize** a single numerical target that represents the yield of a -chemical reaction. - -In BayBE's language, the reaction yield can be represented as a [`NumericalTarget`](baybe.targets.numerical) -object: +In BayBE's language, the `Yield` can be represented as a +[`NumericalTarget`](baybe.targets.numerical) which we pass into an `Objective`. ```python from baybe.targets import NumericalTarget +from baybe.objective import Objective target = NumericalTarget( name="Yield", mode="MAX", ) -``` - -We wrap the target object in an optimization [`Objective`](baybe.objective.Objective), to inform BayBE -that this is the only target we would like to consider: - -```python -from baybe.objective import Objective - objective = Objective(mode="SINGLE", targets=[target]) ``` In cases where we need to consider multiple (potentially competing) targets, the -role of the [`Objective`](baybe.objective.Objective) is to define how these targets should be balanced. -For more details, see [the targets section of the user guide](docs/userguide/targets.md). +role of the [`Objective`](baybe.objective.Objective) is to define additional settings, +e.g. how these targets should be balanced. In `SINGLE` mode, however, there are no +additional settings. For more details, see +[the targets section of the user guide](docs/userguide/targets.md). ### Defining the Search Space Next, we inform BayBE about the available "control knobs", that is, the underlying -system parameters we can tune to optimize our targets. -This also involves specifying their ranges and other parameter-specific details. +system parameters we can tune to optimize our targets. This also involves specifying +their values/ranges and other parameter-specific details. -For our reaction example, we assume that we can control the following three quantities: +For our example, we assume that we can control the following three quantities: ```python from baybe.parameters import CategoricalParameter, NumericalDiscreteParameter, SubstanceParameter @@ -174,46 +131,37 @@ parameters = [ CategoricalParameter( name="Granularity", values=["coarse", "medium", "fine"], - encoding="OHE", + encoding="OHE", # one-hot encoding of categories ), NumericalDiscreteParameter( name="Pressure[bar]", values=[1, 5, 10], - tolerance=0.2, + tolerance=0.2, # allows experimental inaccuracies up to 0.2 when reading values ), SubstanceParameter( name="Solvent", - data={"Solvent A": "COC", "Solvent B": "CCC", "Solvent C": "O", - "Solvent D": "CS(=O)C"}, - encoding="MORDRED", + data={"Solvent A": "COC", "Solvent B": "CCC", # label-SMILES pairs + "Solvent C": "O", "Solvent D": "CS(=O)C"}, + encoding="MORDRED", # chemical encoding via mordred package ), ] -``` - -Note that each parameter is of a different **type** and thus requires its own -type-specific settings. In particular case above, for instance: -* `encoding=OHE` activates one-hot-encoding for the categorical parameter "Granularity". -* `tolerance=0.2` allows experimental inaccuracies up to 0.2 when reading values for - "Pressure[bar]". -* `encoding=MORDRED`triggers computation of MORDRED cheminformatics descriptors for - the substance parameter "Solvent". +constraints = None +``` For more parameter types and their details, see [parameters section of the user guide](docs/userguide/parameters). Additionally, we can define a set of constraints to further specify allowed ranges and -relationships between our parameters. -Details can be found in [the constraints section of the user guids](docs/userguide/constraints). -In this example, we assume no further constraints and explicitly indicate this with an -empty variable, for the sake of demonstration: +relationships between our parameters. Details can be found in +[the constraints section of the user guide](docs/userguide/constraints). In this +example, we assume no further constraints and explicitly indicate this with an empty +variable `constraints`. -```python -constraints = None -``` With the parameter and constraint definitions at hand, we can now create our -[`SearchSpace`](baybe.searchspace): +[`SearchSpace`](baybe.searchspace) based on the product of all possible parameter +values: ```python from baybe.searchspace import SearchSpace @@ -224,15 +172,13 @@ searchspace = SearchSpace.from_product(parameters, constraints) ### Optional: Defining the Optimization Strategy As an optional step, we can specify details on how the optimization should be -conducted. -If omitted, BayBE will choose a default setting. +conducted. If omitted, BayBE will choose a default setting. -For our chemistry example, we combine two selection strategies: +For our example, we combine two selection strategies: 1. In cases where no measurements have been made prior to the interaction with BayBE, - a random experiment selection strategy is used to produce initial recommendations. -2. As soon as the first measurements are available, we switch to a Bayesian approach - where points are selected greedily from a probabilistic prediction model. + a selection via `initial_recommender` is used. +2. As soon as the first measurements are available, we switch to `recommender`. For more details on the different strategies, their underlying algorithmic details, and their configuration settings, see @@ -240,19 +186,17 @@ details, and their configuration settings, see ```python from baybe.strategies import TwoPhaseStrategy -from baybe.recommenders import SequentialGreedyRecommender, RandomRecommender +from baybe.recommenders import SequentialGreedyRecommender, FPSRecommender strategy = TwoPhaseStrategy( - initial_recommender=RandomRecommender(), - recommender=SequentialGreedyRecommender(), + initial_recommender=FPSRecommender(), # farthest point sampling + recommender=SequentialGreedyRecommender(), # Bayesian model-based optimization ) ``` ### The Optimization Loop -Having provided the answers to [all questions above](#getting-started), we can now -construct a BayBE object that brings all -pieces of the puzzle together: +We can now construct a BayBE object that brings all pieces of the puzzle together: ```python from baybe import Campaign @@ -267,16 +211,11 @@ In particular: * We can `add_measurements` for certain experimental settings to BayBE's database. Note that these two steps can be performed in any order. -In particular, available measurement data can be submitted at any time. -Also, we can start the interaction with either command and repeat the same type of -command immediately after its previous call, e.g., if the required number of -recommendations has changed. - -The following illustrates one such possible sequence of interactions. -Let us first ask for an initial set of recommendations: +In particular, available measurements can be submitted at any time and also several +times before querying the next recommendations. ```python -df = campaign.recommend(batch_quantity=5) +df = campaign.recommend(batch_quantity=3) ``` For a particular random seed, the result could look as follows: @@ -286,19 +225,18 @@ For a particular random seed, the result could look as follows: | medium | 1 | Solvent B | | medium | 5 | Solvent D | | fine | 5 | Solvent C | -| fine | 5 | Solvent A | -| medium | 10 | Solvent B | After having conducted the corresponding experiments, we can add our measured -yields to the table and feed it back to BayBE: +targets to the table and feed it back to BayBE: ```python -df["Yield"] = [79, 54, 59, 95, 84] +df["Yield"] = [79.8, 54.1, 59.4] campaign.add_measurements(df) ``` With the newly arrived data, BayBE will update its internal state and can produce a -refined design for the next iteration. +refined design for the next iteration. This loop would typically continue until a +desired target value has been achieved in the experiment. ## Known Issues From b62778601cb523d84c3c14d34e32a7ece7057f08 Mon Sep 17 00:00:00 2001 From: Adrian Sosic Date: Wed, 29 Nov 2023 08:40:47 +0100 Subject: [PATCH 11/17] Add commas and apply some minor fixes --- README.md | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index e8173574d..15f9b2810 100644 --- a/README.md +++ b/README.md @@ -68,11 +68,11 @@ pip install -e '.[dev]' ``` ### Optional Dependencies -There are several dependency groups that can be installed during pip installation like +There are several dependency groups that can be installed during pip installation, like ```bash pip install baybe[test,lint] # will install baybe with additional dependency groups `test` and `lint` ``` -To get the most out of `baybe` we recommend to install at least +To get the most out of `baybe`, we recommend to install at least ```bash pip install baybe[chem,simulation] ``` @@ -97,7 +97,7 @@ a single target called `Yield`. ### Defining the Optimization Objective In BayBE's language, the `Yield` can be represented as a -[`NumericalTarget`](baybe.targets.numerical) which we pass into an `Objective`. +[`NumericalTarget`](baybe.targets.numerical), which we pass into an `Objective`. ```python from baybe.targets import NumericalTarget @@ -145,28 +145,24 @@ parameters = [ encoding="MORDRED", # chemical encoding via mordred package ), ] - -constraints = None ``` -For more parameter types and their details, see +For more parameter types and their details, see the [parameters section of the user guide](docs/userguide/parameters). Additionally, we can define a set of constraints to further specify allowed ranges and relationships between our parameters. Details can be found in [the constraints section of the user guide](docs/userguide/constraints). In this -example, we assume no further constraints and explicitly indicate this with an empty -variable `constraints`. - +example, we assume no further constraints. With the parameter and constraint definitions at hand, we can now create our -[`SearchSpace`](baybe.searchspace) based on the product of all possible parameter -values: +[`SearchSpace`](baybe.searchspace) based on the Cartesian product of all possible +parameter values: ```python from baybe.searchspace import SearchSpace -searchspace = SearchSpace.from_product(parameters, constraints) +searchspace = SearchSpace.from_product(parameters) ``` ### Optional: Defining the Optimization Strategy @@ -196,7 +192,7 @@ strategy = TwoPhaseStrategy( ### The Optimization Loop -We can now construct a BayBE object that brings all pieces of the puzzle together: +We can now construct a campaign object that brings all pieces of the puzzle together: ```python from baybe import Campaign @@ -208,7 +204,8 @@ With this object at hand, we can start our experimentation cycle. In particular: * We can ask BayBE to `recommend` new experiments. -* We can `add_measurements` for certain experimental settings to BayBE's database. +* We can `add_measurements` for certain experimental settings to the campaign's + database. Note that these two steps can be performed in any order. In particular, available measurements can be submitted at any time and also several @@ -227,16 +224,16 @@ For a particular random seed, the result could look as follows: | fine | 5 | Solvent C | After having conducted the corresponding experiments, we can add our measured -targets to the table and feed it back to BayBE: +targets to the table and feed it back to the campaign: ```python df["Yield"] = [79.8, 54.1, 59.4] campaign.add_measurements(df) ``` -With the newly arrived data, BayBE will update its internal state and can produce a -refined design for the next iteration. This loop would typically continue until a -desired target value has been achieved in the experiment. +With the newly arrived data, BayBE can produce a refined design for the next iteration. +This loop would typically continue until a desired target value has been achieved in +the experiment. ## Known Issues From 6b310c86b7c5dfa824b7e4719cf28a85b55b037d Mon Sep 17 00:00:00 2001 From: Adrian Sosic Date: Wed, 29 Nov 2023 09:11:13 +0100 Subject: [PATCH 12/17] Refine installation instructions --- README.md | 29 +++++++++++++++++++++-------- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 15f9b2810..8fb6d3dfc 100644 --- a/README.md +++ b/README.md @@ -47,10 +47,25 @@ pip install baybe conda install --channel=conda-forge baybe ``` -### From Repository +A certain released version of the package can installed by specifying the +corresponding version tag in the form `baybe==x.y.z`. + +### From GitHub If you need finer control and would like to install a specific commit that has not been released under a certain version tag, you can do so by installing BayBE directly from -the repository. +GitHub via git and specifying the corresponding +[git ref](https://pip.pypa.io/en/stable/topics/vcs-support/#git). + +For instance, to install the latest commit of the main branch, run: + +```bash +pip install git+https://github.com/emdgroup/BayBE.git@main +``` + + +### From Local Clone + +Alternatively, you can install the package from your own local copy. First, clone the repository, navigate to the repository root folder, check out the desired commit, and run: @@ -58,17 +73,15 @@ desired commit, and run: pip install . ``` -There are additional dependencies that can be installed corresponding to linters, -formatters etc. (e.g. `dev`). A developer would typically also install the package in -editable mode ('-e') which ensures that changes to the code do not require a -reinstallation. +A developer would typically also install the package in editable mode ('-e'), +which ensures that changes to the code do not require a reinstallation. ```bash -pip install -e '.[dev]' +pip install -e . ``` ### Optional Dependencies -There are several dependency groups that can be installed during pip installation, like +There are several dependency groups that can be selected during pip installation, like ```bash pip install baybe[test,lint] # will install baybe with additional dependency groups `test` and `lint` ``` From 091aaf9cfbae39fc6f5e57347a9cd97fc09a63f8 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Wed, 29 Nov 2023 13:54:51 +0100 Subject: [PATCH 13/17] Fix typos --- CHANGELOG.md | 4 ++-- baybe/telemetry.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe0130675..d3e4ee0f3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Enabled passing optional arguments to `tox -e docs` calls - Logo and banner images -### -- reworked README +### Changed +- reworked README for GitHub landing page ### Changed - Now has concise contribution guidelines diff --git a/baybe/telemetry.py b/baybe/telemetry.py index a569f8ef0..8bd036f3e 100644 --- a/baybe/telemetry.py +++ b/baybe/telemetry.py @@ -18,7 +18,7 @@ * How often initial measurements are added before recommendations were calculated ("naked initial measurements") * The fraction of measurements added that correspond to previous recommendations - * Each measurement is associated with an irreversible has of the user- and hostname + * Each measurement is associated with an irreversible hash of the user- and hostname **The following environment variables control the behavior of BayBE telemetry:** From cb3397a739b54dfb22503c2dea45e499da9eebaa Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Wed, 29 Nov 2023 13:55:51 +0100 Subject: [PATCH 14/17] Refine README.md --- README.md | 39 ++++++++++++++++++++++++--------------- _typos.toml | 2 -- 2 files changed, 24 insertions(+), 17 deletions(-) delete mode 100644 _typos.toml diff --git a/README.md b/README.md index 8fb6d3dfc..2cfca477f 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,18 @@

- -[![ci](https://github.com/emdgroup/BayBE/actions/workflows/ci.yml/badge.svg)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Aci.yml) -[![regular](https://github.com/emdgroup/BayBE/actions/workflows/regular.yml/badge.svg)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Aregular.yml) - -Conda Version - - - - - -[![Logo](https://raw.githubusercontent.com/emdgroup/baybe/main/docs/images/banner2.svg)](https://github.com/emdgroup/baybe) + +[![CI](https://img.shields.io/github/actions/workflow/status/emdgroup/BayBE/ci.yml?style=flat-square&label=CI&labelColor=0f69af&color=ffdcb9)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Aci.yml) +[![Regular](https://img.shields.io/github/actions/workflow/status/emdgroup/BayBE/regular.yml?style=flat-square&label=Regular%20Check&labelColor=0f69af&color=ffdcb9)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Aregular.yml) +[![Docs](https://img.shields.io/github/actions/workflow/status/emdgroup/BayBE/docs.yml?style=flat-square&label=Docs&labelColor=0f69af&color=ffdcb9)](https://github.com/emdgroup/BayBE/actions?query=workflow%3Adocs.yml) + +[![Supported Python version](https://img.shields.io/pypi/pyversions/baybe?style=flat-square&label=Supported%20Python%20Versions&labelColor=96d7d2&color=ffdcb9)](https://pypi.org/project/baybe/) +[![PyPI version](https://img.shields.io/pypi/v/baybe.svg?style=flat-square&label=PyPI%20Version&labelColor=96d7d2&color=ffdcb9)](https://pypi.org/project/baybe/) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/baybe.svg?style=flat-square&label=Conda%20Forge%20Version&labelColor=96d7d2&color=ffdcb9)](https://anaconda.org/conda-forge/baybe) +[![Issues](https://img.shields.io/github/issues/emdgroup/BayBE?style=flat-square&label=Issues&labelColor=96d7d2&color=ffdcb9)](https://github.com/emdgroup/BayBE/issues) +[![PRs](https://img.shields.io/github/issues-pr/emdgroup/BayBE?style=flat-square&label=PRs&labelColor=96d7d2&color=ffdcb9)](https://github.com/emdgroup/BayBE/pulls) +[![License](https://shields.io/badge/License-Apache%202.0-green.svg?style=flat-square&labelColor=96d7d2&color=ffdcb9)](http://www.apache.org/licenses/LICENSE-2.0) + +[![Logo](https://raw.githubusercontent.com/emdgroup/BayBE/main/docs/images/banner2.svg)](https://github.com/emdgroup/baybe) Documentation  โ€ข  @@ -21,8 +23,8 @@ # BayBE โ€” A Bayesian Back End for Design of Experiments -The **Bay**esian **B**ack **E**nd provides a general-purpose toolbox for Bayesian Design of -Experiments, focusing on additions that enable real-world experimental campaigns. +The Bayesian Back End (**BayBE**) provides a general-purpose toolbox for Bayesian Design +of Experiments, focusing on additions that enable real-world experimental campaigns. Besides functionality to perform a typical recommend-measure loop, BayBE's highlights are: - Custom parameter encodings: Improve your campaign with domain knowledge @@ -33,7 +35,7 @@ Besides functionality to perform a typical recommend-measure loop, BayBE's highl - Transfer learning: Mix data from multiple campaigns and accelerate optimization - Comprehensive backtest, simulation and imputation utilities: Benchmark and find your best settings - Fully typed and hypothesis-tested: Robust code base -- The entire state of your campaign is fully de-/serializable: Useful for storing results in databases +- All objects are fully de-/serializable: Useful for storing results in databases or use in wrappers like APIs ## Installation ### From Package Index @@ -44,7 +46,7 @@ pip install baybe ``` ```bash -conda install --channel=conda-forge baybe +conda install -c conda-forge baybe ``` A certain released version of the package can installed by specifying the @@ -80,6 +82,13 @@ which ensures that changes to the code do not require a reinstallation. pip install -e . ``` +If you need to add additional dependencies make sure to use the correct syntax +including `''`: + +```bash +pip install -e '.[dev]' +``` + ### Optional Dependencies There are several dependency groups that can be selected during pip installation, like ```bash diff --git a/_typos.toml b/_typos.toml deleted file mode 100644 index 359d0fd56..000000000 --- a/_typos.toml +++ /dev/null @@ -1,2 +0,0 @@ -[type.md] -extend-ignore-identifiers-re = ['^E*nd$'] # ignore `**E**nd` in README.md \ No newline at end of file From 5ee5fe11313c71165c438bdb683b9e46c4ecc839 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Wed, 29 Nov 2023 15:05:22 +0100 Subject: [PATCH 15/17] Change folder for images --- README.md | 2 +- docs/{images => _static}/banner1.svg | 0 docs/{images => _static}/banner2.svg | 0 docs/{images => _static}/logo1.svg | 0 docs/{images => _static}/logo2.svg | 0 5 files changed, 1 insertion(+), 1 deletion(-) rename docs/{images => _static}/banner1.svg (100%) rename docs/{images => _static}/banner2.svg (100%) rename docs/{images => _static}/logo1.svg (100%) rename docs/{images => _static}/logo2.svg (100%) diff --git a/README.md b/README.md index 2cfca477f..bacf5ff5d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ [![PRs](https://img.shields.io/github/issues-pr/emdgroup/BayBE?style=flat-square&label=PRs&labelColor=96d7d2&color=ffdcb9)](https://github.com/emdgroup/BayBE/pulls) [![License](https://shields.io/badge/License-Apache%202.0-green.svg?style=flat-square&labelColor=96d7d2&color=ffdcb9)](http://www.apache.org/licenses/LICENSE-2.0) -[![Logo](https://raw.githubusercontent.com/emdgroup/BayBE/main/docs/images/banner2.svg)](https://github.com/emdgroup/baybe) +[![Logo](https://raw.githubusercontent.com/emdgroup/BayBE/main/docs/_static/banner2.svg)](https://github.com/emdgroup/BayBE) Documentation  โ€ข  diff --git a/docs/images/banner1.svg b/docs/_static/banner1.svg similarity index 100% rename from docs/images/banner1.svg rename to docs/_static/banner1.svg diff --git a/docs/images/banner2.svg b/docs/_static/banner2.svg similarity index 100% rename from docs/images/banner2.svg rename to docs/_static/banner2.svg diff --git a/docs/images/logo1.svg b/docs/_static/logo1.svg similarity index 100% rename from docs/images/logo1.svg rename to docs/_static/logo1.svg diff --git a/docs/images/logo2.svg b/docs/_static/logo2.svg similarity index 100% rename from docs/images/logo2.svg rename to docs/_static/logo2.svg From 0ca6b9894d620b7aaa0d58b11dc2abf09193f862 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Wed, 29 Nov 2023 16:52:04 +0100 Subject: [PATCH 16/17] Fix lexer --- baybe/telemetry.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/baybe/telemetry.py b/baybe/telemetry.py index 8bd036f3e..02908d297 100644 --- a/baybe/telemetry.py +++ b/baybe/telemetry.py @@ -45,7 +45,7 @@ If you wish to disable logging, you can set the following environment variable: -.. code-block:: terminal +.. code-block:: console export BAYBE_TELEMETRY_ENABLED=false @@ -60,7 +60,7 @@ Telemetry can be re-enabled by simply removing the variable: -.. code-block:: terminal +.. code-block:: console unset BAYBE_TELEMETRY_ENABLED From 3e81338ca350675f46e89a91de41f763d7401317 Mon Sep 17 00:00:00 2001 From: Adrian Sosic Date: Wed, 29 Nov 2023 20:27:12 +0100 Subject: [PATCH 17/17] Fix typos --- CHANGELOG.md | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3e4ee0f3..a63857e08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Logo and banner images ### Changed -- reworked README for GitHub landing page +- Reworked README for GitHub landing page ### Changed - Now has concise contribution guidelines diff --git a/README.md b/README.md index bacf5ff5d..5fb482795 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ which ensures that changes to the code do not require a reinstallation. pip install -e . ``` -If you need to add additional dependencies make sure to use the correct syntax +If you need to add additional dependencies, make sure to use the correct syntax including `''`: ```bash