From 1ff915fdf235d015519f5950fa402a4cfba46085 Mon Sep 17 00:00:00 2001 From: "Alexander V. Hopp" Date: Tue, 5 Dec 2023 10:04:04 +0100 Subject: [PATCH 1/3] Fix in-/external links in CONTRIBUTING --- CONTRIBUTING.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e00fc842a9..9f39b1c3a4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -47,7 +47,7 @@ we recommend the following workflow: 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 retrieve all available environments via `tox list`. - For more information, see our [README about tests](tests/README.md). + For more information, see our [README about tests](https://github.com/emdgroup/baybe/blob/main/tests/README.md). For instance, running all code tests in Python 3.11 can be achieved via: ```console @@ -70,6 +70,7 @@ we recommend the following workflow: 1. Open a pull request via Github's web page. +(developer-tools)= ## Developer Tools In order to maintain a high code quality, we use a variety of code developer tools. @@ -98,7 +99,7 @@ tox -e ``` where `` is any of the environment names found via `tox list`. - +(code-design)= ## Code Design When reading BayBE's code, you will notice certain re-occurring design patterns. @@ -121,7 +122,7 @@ make sure that the newly written code is well integrated into the existing packa module hierarchy. In particular, public functionality should be imported into the appropriate high-level namespaces for easier user import. For an example, see our -[parameter namespace](baybe/parameters/__init__.py). +[parameter namespace](https://github.com/emdgroup/baybe/blob/main/baybe/parameters/__init__.py). ## Writing Docstrings From 172ab4f8da9aafab5f0ad7112e6951b0fe9626a6 Mon Sep 17 00:00:00 2001 From: "Alexander V. Hopp" Date: Tue, 5 Dec 2023 10:09:11 +0100 Subject: [PATCH 2/3] Fix typo in link --- docs/userguide/campaigns.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/campaigns.md b/docs/userguide/campaigns.md index bdee4b95cd..1278e9590d 100644 --- a/docs/userguide/campaigns.md +++ b/docs/userguide/campaigns.md @@ -12,7 +12,7 @@ series of measurements and the iterative sequence of events involved. To construct a new campaign, it is necessary to provide two objects. 1. **A search space:** The parameter space in which the campaign operates. It can be a purely discrete, purely continuous or hybir space. We refer to the [`Searchspace`](baybe.searchspace.core.SearchSpace) class resp. the corresponding [user guide](./searchspace) for more details. -2. **An objective:** The optimization objective. It is possible to either optimize a single target or to combine different targets. We refer to the [`Objective`](baybe.objective.Objective) class resp. the corresponding [user guide](./objectives) for more details. +2. **An objective:** The optimization objective. It is possible to either optimize a single target or to combine different targets. We refer to the [`Objective`](baybe.objective.Objective) class resp. the corresponding [user guide](./objective) for more details. The following additional aspects are available to further specify a campaign: * **A strategy:**: The strategy that is used during the campaign. As a default, a [`TwoPhaseStrategy`](baybe.strategies.composite.TwoPhaseStrategy) is employed. For more details on strategies, see [here](./strategy). From eca7378989823e8d4cfe8011a6991c3957fc4a0b Mon Sep 17 00:00:00 2001 From: "Alexander V. Hopp" Date: Tue, 5 Dec 2023 10:10:48 +0100 Subject: [PATCH 3/3] Add explicit links to headings --- docs/userguide/constraints.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/userguide/constraints.md b/docs/userguide/constraints.md index 9123680a21..bc5202b9a2 100644 --- a/docs/userguide/constraints.md +++ b/docs/userguide/constraints.md @@ -27,6 +27,7 @@ Not all surrogate models are able to treat continuous constraints. In such situa the constraints are currently silently ignored. ``` +(CLEQ)= ### ``ContinuousLinearEqualityConstraint`` This linear constraint asserts that the following equation is true (up to numerical rounding errors): @@ -68,7 +69,7 @@ both sides, i.e. the coefficients and rhs, by -1. ``` Let us amend the example from -[`ContinuousLinearEqualityConstraint`](#continuouslinearequalityconstraint) and assume +[`ContinuousLinearEqualityConstraint`](#CLEQ) and assume that there is always a fourth component to the mixture which serves as a "filler". In such a case we might want to ensure that the first three components only make up to 80% of the mixture. @@ -147,7 +148,7 @@ DiscreteExcludeConstraint( ### ``DiscreteSumConstraint`` and ``DiscreteProductConstraint`` These constraints constrain sums or products of numerical parameters. In the example -from [``ContinuousLinearEqualityConstraint``](#continuouslinearequalityconstraint) we +from [``ContinuousLinearEqualityConstraint``](#CLEQ) we had three continuous parameters ``x_1``, ``x_2`` and ``x_3`` which needed to sum up to 1.0. If these parameters were instead discrete, the corresponding constraint would look like: