From 3be3612b68b4cf0e0408816cb1dfdcb9b515cb81 Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 09:19:31 +0100 Subject: [PATCH 01/14] Add missing quotes around dependency groups --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5fb482795..d23c0aaaf 100644 --- a/README.md +++ b/README.md @@ -92,11 +92,11 @@ pip install -e '.[dev]' ### Optional Dependencies 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` +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 ```bash -pip install baybe[chem,simulation] +pip install 'baybe[chem,simulation]' ``` The available groups are: From 3b3b3892d38346b2609ba25299deeeb0c96a4e34 Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 09:25:13 +0100 Subject: [PATCH 02/14] Add link to ONNX --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d23c0aaaf..e6a124f2a 100644 --- a/README.md +++ b/README.md @@ -105,7 +105,7 @@ The available groups are: - `examples`: Required for running the examples/streamlit. - `lint`: Required for linting and formatting. - `mypy`: Required for static type checking. -- `onnx`: Required for using custom surrogate models in ONNX format. +- `onnx`: Required for using custom surrogate models in [ONNX format](https://onnx.ai). - `simulation`: Enabling the [`simulation`](baybe.simulation) module. - `test`: Required for running the tests. - `dev`: All of the above plus `tox` and `pip-audit`. For code contributors. From c873f2701af9da0e6633d5480f7a9f61c90b7ddd Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 10:23:06 +0100 Subject: [PATCH 03/14] Replace "BayBE" with "baybe" in GitHub links --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index e6a124f2a..2f1a5d209 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,18 @@

-[![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) +[![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) +[![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/_static/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  •  @@ -61,7 +61,7 @@ GitHub via git and specifying the corresponding For instance, to install the latest commit of the main branch, run: ```bash -pip install git+https://github.com/emdgroup/BayBE.git@main +pip install git+https://github.com/emdgroup/baybe.git@main ``` From a940e44a0354fe882e442ae4d85651eee6bc9d69 Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 10:34:15 +0100 Subject: [PATCH 04/14] Fix badges and top links --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 2f1a5d209..79ea33cdc 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,22 @@

-[![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) +[![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/workflows/ci.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/workflows/regular.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/workflows/docs.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) +[![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/_static/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 +Documentation  •  -User Guide +User Guide  •  Contribute
From 7621ea01ebe1bafe7a82ea7c3d610a971e92ed36 Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 12:10:28 +0100 Subject: [PATCH 05/14] Add homepage link --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 79ea33cdc..857340c20 100644 --- a/README.md +++ b/README.md @@ -14,10 +14,12 @@ [![Logo](https://raw.githubusercontent.com/emdgroup/baybe/main/docs/_static/banner2.svg)](https://github.com/emdgroup/baybe/) -Documentation +Homepage  •  User Guide  •  +Documentation + •  Contribute
From 1e64f67cc84274ef70bd639d53da0bf31ee2be24 Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 12:46:37 +0100 Subject: [PATCH 06/14] Add "Objective" section to user guide --- docs/userguide/objective.md | 4 ++++ docs/userguide/userguide.md | 1 + 2 files changed, 5 insertions(+) create mode 100644 docs/userguide/objective.md diff --git a/docs/userguide/objective.md b/docs/userguide/objective.md new file mode 100644 index 000000000..f8d734d5f --- /dev/null +++ b/docs/userguide/objective.md @@ -0,0 +1,4 @@ +# Objective + +This page will soon contain information about objectives. +In the meantime, please see the [examples](../../examples/examples) instead. \ No newline at end of file diff --git a/docs/userguide/userguide.md b/docs/userguide/userguide.md index 38810a2a7..00534e5bb 100644 --- a/docs/userguide/userguide.md +++ b/docs/userguide/userguide.md @@ -7,6 +7,7 @@ In the meantime, we refer to the [examples](../../examples/examples) instead. ```{toctree} Campaigns Constraints +Objective Parameters Recommender Search spaces From ca9d1695284e3270ee31382baabcd9cca521a5d0 Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 12:47:14 +0100 Subject: [PATCH 07/14] Fix documentation links in README.md --- README.md | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 857340c20..1726f6a07 100644 --- a/README.md +++ b/README.md @@ -102,13 +102,13 @@ pip install 'baybe[chem,simulation]' ``` The available groups are: -- `chem`: Cheminformatics utilities (e.g. for the [`SubstanceParameter`](baybe.parameters.substance.SubstanceParameter)). +- `chem`: Cheminformatics utilities (e.g. for the [`SubstanceParameter`](https://emdgroup.github.io/baybe/_autosummary/baybe.parameters.substance.SubstanceParameter.html#baybe.parameters.substance.SubstanceParameter)). - `docs`: Required for creating the documentation. - `examples`: Required for running the examples/streamlit. - `lint`: Required for linting and formatting. - `mypy`: Required for static type checking. - `onnx`: Required for using custom surrogate models in [ONNX format](https://onnx.ai). -- `simulation`: Enabling the [`simulation`](baybe.simulation) module. +- `simulation`: Enabling the [`simulation`](https://emdgroup.github.io/baybe/_autosummary/baybe.simulation.html) module. - `test`: Required for running the tests. - `dev`: All of the above plus `tox` and `pip-audit`. For code contributors. @@ -121,7 +121,9 @@ 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`](https://emdgroup.github.io/baybe/userguide/targets.html), +which we pass into an +[`Objective`](https://emdgroup.github.io/baybe/userguide/objective.html). ```python from baybe.targets import NumericalTarget @@ -135,10 +137,11 @@ 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 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). +role of the [`Objective`](https://emdgroup.github.io/baybe/userguide/objective.html) +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 objective section of the user guide](https://emdgroup.github.io/baybe/userguide/objective.html). ### Defining the Search Space @@ -172,16 +175,16 @@ parameters = [ ``` For more parameter types and their details, see the -[parameters section of the user guide](docs/userguide/parameters). +[parameters section of the user guide](https://emdgroup.github.io/baybe/userguide/parameters.html). 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. +[the constraints section of the user guide](https://emdgroup.github.io/baybe/userguide/constraints.html). +In this 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 Cartesian product of all possible -parameter values: +[`SearchSpace`](https://emdgroup.github.io/baybe/userguide/searchspace.html) +based on the Cartesian product of all possible parameter values: ```python from baybe.searchspace import SearchSpace @@ -202,7 +205,7 @@ For our example, we combine two selection strategies: For more details on the different strategies, their underlying algorithmic details, and their configuration settings, see -[the strategies section of the user guide](docs/userguide/strategy). +[the strategies section of the user guide](https://emdgroup.github.io/baybe/userguide/strategy.html). ```python from baybe.strategies import TwoPhaseStrategy From 27d73dc064e779ae8cadbeedd2919a87a28efa3b Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 12:55:35 +0100 Subject: [PATCH 08/14] Add GitHub toc entry --- docs/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/index.md b/docs/index.md index 030896bfa..726970a17 100644 --- a/docs/index.md +++ b/docs/index.md @@ -34,6 +34,7 @@ Contribute Known Issues FAQ Changelog + Github Contributors License ``` From d5d8418f852c726328697438a6be4a35175adbdd Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Fri, 1 Dec 2023 16:59:43 +0100 Subject: [PATCH 09/14] Add whitespace for proper rendering of links --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 1726f6a07..0dcfa8dd9 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,7 @@ [![Logo](https://raw.githubusercontent.com/emdgroup/baybe/main/docs/_static/banner2.svg)](https://github.com/emdgroup/baybe/) +  Homepage  •  User Guide @@ -21,6 +22,7 @@ Documentation  •  Contribute +  # BayBE — A Bayesian Back End for Design of Experiments From 4daeed62a5f120e25b0f6030a000fe7fc7640651 Mon Sep 17 00:00:00 2001 From: Martin Fitzner Date: Sat, 2 Dec 2023 23:13:19 +0100 Subject: [PATCH 10/14] Fix tox instructions --- CONTRIBUTING.md | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index df6c08ea6..f3e986728 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -43,15 +43,23 @@ we recommend the following workflow: 1. Optional but recommended to prevent complaints from our CI pipeline: Test your code. - Testing against a single python can be achieved via `tox -e `. For instance: - ```bash - tox -e py311 + There are several test environments you can run via `tox`, each corresponding to a + [developer tool](#developer-tools) in a certain Python version. You can see all + available environments via `tox list`. + + For instance, running all code tests in Python 3.11 can be achieved via: + ```console + tox -e fulltest-py311 ``` - If you want to challenge your machine, you can run all version tests in parallel via: - ```bash + If you want to challenge your machine, you can run all checks in all Python versions + in parallel via: + ```console tox -p ``` + + This can be considered the ultimate one-stop check to make sure your code is ready + for merge. 1. Push the updated branch back to your fork: ```console From 6b97f328d134884f4fa683f72f476c27af6d004a Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Mon, 4 Dec 2023 09:08:45 +0100 Subject: [PATCH 11/14] Add link to tests/README.md --- CONTRIBUTING.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index f3e986728..e00fc842a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -41,11 +41,13 @@ we recommend the following workflow: 1. **Implement your changes.** -1. Optional but recommended to prevent complaints from our CI pipeline: Test your code. +1. Optional but recommended to prevent complaints from our CI pipeline: + **Test your code.** There are several test environments you can run via `tox`, each corresponding to a - [developer tool](#developer-tools) in a certain Python version. You can see all - available environments via `tox list`. + [developer tool](#developer-tools) in a certain Python version. + You can retrieve all available environments via `tox list`. + For more information, see our [README about tests](tests/README.md). For instance, running all code tests in Python 3.11 can be achieved via: ```console From 45e0af40efe18a2be7c255a46dbfe84a03cd65aa Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Mon, 4 Dec 2023 09:14:19 +0100 Subject: [PATCH 12/14] Fix link to known issues --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0dcfa8dd9..c5f7402e4 100644 --- a/README.md +++ b/README.md @@ -266,7 +266,7 @@ the experiment. ## Known Issues -A list of know issues can be found [here](docs/known_issues.md). +A list of know issues can be found [here](https://emdgroup.github.io/baybe/known_issues.html). ## License From 94def673b65c2abcd7d0053d091fadce510df36b Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Mon, 4 Dec 2023 09:41:09 +0100 Subject: [PATCH 13/14] Configure linkcheck in GitHub actions * Linkcheck is disabled via an environment variable in CI pipeline, because the relevant pages do not yet exist * Doc generation is added to the regular pipeline to trigger the linkcheck later --- .github/workflows/docs.yml | 3 +++ .github/workflows/regular.yml | 17 +++++++++++++++++ tox.ini | 3 +-- 3 files changed, 21 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 630896857..c80a9635e 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -9,6 +9,9 @@ concurrency: group: ${{ github.workflow }} cancel-in-progress: true +env: + BAYBE_DOCS_LINKCHECK_IGNORE: true # Ignore link checks to github.io (pages might not yet exist) + jobs: build: runs-on: ubuntu-latest diff --git a/.github/workflows/regular.yml b/.github/workflows/regular.yml index 721df8e4b..8c71f6379 100644 --- a/.github/workflows/regular.yml +++ b/.github/workflows/regular.yml @@ -19,6 +19,23 @@ concurrency: cancel-in-progress: true jobs: + + # Warns about broken links in the docs. Especially useful for + # those that point to our own github.io page (linkcheck is disabled in the + # CI pipeline, because the respective pages are yet to be created at that time). + docs: + runs-on: ubuntu-latest + permissions: + contents: read + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: {python-version: "3.11"} + - name: Build Docs + run: | + pip install tox + tox -e docs-py311 + lint: strategy: matrix: diff --git a/tox.ini b/tox.ini index 6c93fc0bb..31fb00965 100644 --- a/tox.ini +++ b/tox.ini @@ -50,5 +50,4 @@ description = Build documentation extras = docs commands = python --version - # TODO: remove --force option once all links are intact - python docs/scripts/convert_code_to_documentation.py --force {posargs} \ No newline at end of file + python docs/scripts/convert_code_to_documentation.py {posargs} \ No newline at end of file From 70347b394768d36d17eaf64ef756f66372d7005a Mon Sep 17 00:00:00 2001 From: AdrianSosic Date: Mon, 4 Dec 2023 10:03:14 +0100 Subject: [PATCH 14/14] Avoid placing links on code expressions --- README.md | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index c5f7402e4..63b599a79 100644 --- a/README.md +++ b/README.md @@ -104,13 +104,13 @@ pip install 'baybe[chem,simulation]' ``` The available groups are: -- `chem`: Cheminformatics utilities (e.g. for the [`SubstanceParameter`](https://emdgroup.github.io/baybe/_autosummary/baybe.parameters.substance.SubstanceParameter.html#baybe.parameters.substance.SubstanceParameter)). +- `chem`: Cheminformatics utilities (e.g. for the `SubstanceParameter`). - `docs`: Required for creating the documentation. - `examples`: Required for running the examples/streamlit. - `lint`: Required for linting and formatting. - `mypy`: Required for static type checking. - `onnx`: Required for using custom surrogate models in [ONNX format](https://onnx.ai). -- `simulation`: Enabling the [`simulation`](https://emdgroup.github.io/baybe/_autosummary/baybe.simulation.html) module. +- `simulation`: Enabling the [simulation](https://emdgroup.github.io/baybe/_autosummary/baybe.simulation.html) module. - `test`: Required for running the tests. - `dev`: All of the above plus `tox` and `pip-audit`. For code contributors. @@ -122,10 +122,8 @@ a single target called `Yield`. ### Defining the Optimization Objective -In BayBE's language, the `Yield` can be represented as a -[`NumericalTarget`](https://emdgroup.github.io/baybe/userguide/targets.html), -which we pass into an -[`Objective`](https://emdgroup.github.io/baybe/userguide/objective.html). +In BayBE's language, the `Yield` can be represented as a `NumericalTarget`, +which we pass into an `Objective`. ```python from baybe.targets import NumericalTarget @@ -139,8 +137,8 @@ objective = Objective(mode="SINGLE", targets=[target]) ``` In cases where we need to consider multiple (potentially competing) targets, the -role of the [`Objective`](https://emdgroup.github.io/baybe/userguide/objective.html) -is to define additional settings, e.g. how these targets should be balanced. +role of the `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 objective section of the user guide](https://emdgroup.github.io/baybe/userguide/objective.html). @@ -185,8 +183,7 @@ relationships between our parameters. Details can be found in In this example, we assume no further constraints. With the parameter and constraint definitions at hand, we can now create our -[`SearchSpace`](https://emdgroup.github.io/baybe/userguide/searchspace.html) -based on the Cartesian product of all possible parameter values: +`SearchSpace` based on the Cartesian product of all possible parameter values: ```python from baybe.searchspace import SearchSpace