Polishing (#527)

optimagic-dev · Aug 26, 2024 · d476eba · d476eba
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diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -2,7 +2,7 @@
 name: PyPI
 on: push
 jobs:
-  build-n-publish-optimagic:
+  build-n-publish:
     name: Build and publish optimagic Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
     steps:
@@ -29,37 +29,3 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN_OPTIMAGIC }}
-  build-n-publish-estimagic:
-    name: Build and publish estimagic Python 🐍 distributions 📦 to PyPI
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.10'
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          toml
-          --user
-      - name: Set name entry in pyproject.toml to estimagic
-        run: >-
-          python .tools/update_name_pyproject.py
-      - name: Add FutureWarning to init files
-        run: >-
-          python .tools/update_init_files.py
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-      - name: Publish distribution 📦 to PyPI
-        if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.tools/update_init_files.py b/.tools/update_init_files.py
diff --git a/.tools/update_name_pyproject.py b/.tools/update_name_pyproject.py
diff --git a/CHANGES.md b/CHANGES.md
@@ -2,7 +2,7 @@
 
 This is a record of all past optimagic releases and what went into them in reverse
 chronological order. We follow [semantic versioning](https://semver.org/) and all
-releases are available on [Anaconda.org](https://anaconda.org/OpenSourceEconomics/optimagic).
+releases are available on [Anaconda.org](https://anaconda.org/optimagic-dev/optimagic).
 
 Following the [scientific python guidelines](https://scientific-python.org/specs/spec-0000/)
 we drop the official support for Python 3.9.

diff --git a/CITATION b/CITATION
@@ -1,19 +1,19 @@
 
-Please use one of the following samples to cite the estimagic version (change
+Please use one of the following samples to cite the optimagic version (change
 x.y) from this installation
 
 Text:
 
 [optimagic]  optimagic x.y, 2024
-Janos Gabler, https://github.com/OpenSourceEconomics/optimagic
+Janos Gabler, https://github.com/optimagic-dev/optimagic
 
 BibTeX:
 
 @Unpublished{Gabler2024,
       Title  = {optimagic: A library for nonlinear optimization},
       Author = {Janos Gabler},
       Year   = {2024},
-      Url    = {https://github.com/OpenSourceEconomics/optimagic}
+      Url    = {https://github.com/optimagic-dev/optimagic}
     }
 
 If you are unsure about which version of optimagic you are using run: `conda list optimagic`.
diff --git a/README.md b/README.md
@@ -1,17 +1,17 @@
 # optimagic
 
 ![PyPI - Version](https://img.shields.io/pypi/v/optimagic)
-[![image](https://img.shields.io/pypi/pyversions/estimagic)](https://pypi.org/project/estimagic)
-[![image](https://img.shields.io/conda/vn/conda-forge/estimagic.svg)](https://anaconda.org/conda-forge/estimagic)
-[![image](https://img.shields.io/conda/pn/conda-forge/estimagic.svg)](https://anaconda.org/conda-forge/estimagic)
-[![image](https://img.shields.io/pypi/l/estimagic)](https://pypi.org/project/estimagic)
-[![image](https://readthedocs.org/projects/estimagic/badge/?version=latest)](https://estimagic.readthedocs.io/en/latest)
-[![image](https://img.shields.io/github/actions/workflow/status/OpenSourceEconomics/estimagic/main.yml?branch=main)](https://github.com/OpenSourceEconomics/estimagic/actions?query=branch%3Amain)
-[![image](https://codecov.io/gh/OpenSourceEconomics/estimagic/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenSourceEconomics/optimagic)
-[![image](https://results.pre-commit.ci/badge/github/OpenSourceEconomics/estimagic/main.svg)](https://github.com/OpenSourceEconomics/optimagic/actions?query=branch%3Amain)
-[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![image](https://img.shields.io/pypi/pyversions/optimagic)](https://pypi.org/project/optimagic)
+[![image](https://img.shields.io/conda/vn/conda-forge/optimagic.svg)](https://anaconda.org/conda-forge/optimagic)
+[![image](https://img.shields.io/conda/pn/conda-forge/optimagic.svg)](https://anaconda.org/conda-forge/optimagic)
+[![image](https://img.shields.io/pypi/l/optimagic)](https://pypi.org/project/optimagic)
+[![image](https://readthedocs.org/projects/optimagic/badge/?version=latest)](https://optimagic.readthedocs.io/en/latest)
+[![image](https://img.shields.io/github/actions/workflow/status/optimagic-dev/optimagic/main.yml?branch=main)](https://github.com/optimagic-dev/optimagic/actions?query=branch%3Amain)
+[![image](https://codecov.io/gh/optimagic-dev/optimagic/branch/main/graph/badge.svg)](https://codecov.io/gh/optimagic-dev/optimagic)
+[![image](https://results.pre-commit.ci/badge/github/optimagic-dev/optimagic/main.svg)](https://results.pre-commit.ci/latest/github/optimagic-dev/optimagic/main)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![image](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
-[![image](https://pepy.tech/badge/estimagic/month)](https://pepy.tech/project/estimagic)
+[![image](https://pepy.tech/badge/optimagic/month)](https://pepy.tech/project/optimagic)
 [![image](https://img.shields.io/badge/NumFOCUS-affiliated%20project-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org/sponsored-projects/affiliated-projects)
 [![image](https://img.shields.io/twitter/follow/aiidateam.svg?style=social&label=Follow)](https://x.com/optimagic)
 
@@ -86,7 +86,7 @@ If you use optimagic for your research, please do not forget to cite it.
   Title  = {optimagic: A library for nonlinear optimization},
   Author = {Janos Gabler},
   Year   = {2022},
-  Url    = {https://github.com/OpenSourceEconomics/optimagic}
+  Url    = {https://github.com/optimagic-dev/optimagic}
 }
 ```
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -81,7 +81,7 @@
 
 extlinks = {
     "ghuser": ("https://github.com/%s", "@"),
-    "gh": ("https://github.com/OpenSourceEconomics/optimagic/pulls/%s", "#"),
+    "gh": ("https://github.com/optimagic-dev/optimagic/pulls/%s", "#"),
 }
 
 intersphinx_mapping = {

diff --git a/docs/source/development/how_to_contribute.md b/docs/source/development/how_to_contribute.md
@@ -13,8 +13,8 @@ ideas and guide the development process from the beginning. You can start a conv
 by posting an issue on GitHub or by emailing [janosg](https://github.com/janosg).
 
 To get familiar with the codebase, we recommend checking out our
-[issue tracker](https://github.com/OpenSourceEconomics/optimagic/issues) for some
-immediate and clearly defined tasks.
+[issue tracker](https://github.com/optimagic-dev/optimagic/issues) for some immediate
+and clearly defined tasks.
 
 ## 2. Before you start
 
@@ -30,11 +30,11 @@ contribution process (see Notes below).
 
 ## 3. Step-by-step guide
 
-1. Fork the [optimagic repository](https://github.com/OpenSourceEconomics/optimagic/).
-   This action creates a copy of the repository with write access for you.
+1. Fork the [optimagic repository](https://github.com/optimagic-dev/optimagic/). This
+   action creates a copy of the repository with write access for you.
 
 ```{note}
-For regular contributors: **Clone** the [repository](https://github.com/OpenSourceEconomics/optimagic/) to your local machine and create a new branch for implementing your changes. You can push your branch directly to the remote optimagic repository and open a PR from there.
+For regular contributors: **Clone** the [repository](https://github.com/optimagic-dev/optimagic/) to your local machine and create a new branch for implementing your changes. You can push your branch directly to the remote optimagic repository and open a PR from there.
 ```
 
 2. Clone your forked repository to your disk. This is where you'll make all your
@@ -110,7 +110,7 @@ Skip the next paragraph if you haven't worked on the documentation.
    ```
 
    Follow the steps outlined in the optimagic
-   [PR template](https://github.com/OpenSourceEconomics/optimagic/blob/main/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
+   [PR template](https://github.com/optimagic-dev/optimagic/blob/main/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
    to describe your contribution, the problem it addresses, and your proposed solution.
 
    Opening a PR initiates a complete CI run, including the `pytest` suite, linters, code

diff --git a/pyproject.toml b/pyproject.toml
@@ -60,9 +60,9 @@ content-type = "text/markdown"
 text = "MIT"
 
 [project.urls]
-Repository = "https://github.com/opensourceeconomics/optimagic"
-Github = "https://github.com/opensourceeconomics/optimagic"
-Tracker = "https://github.com/OpenSourceEconomics/optimagic/issues"
+Repository = "https://github.com/optimagic-dev/optimagic"
+Github = "https://github.com/optimagic-dev/optimagic"
+Tracker = "https://github.com/optimagic-dev/optimagic/issues"
 
 
 # ======================================================================================

diff --git a/src/optimagic/deprecations.py b/src/optimagic/deprecations.py
@@ -45,7 +45,9 @@ def throw_derivative_future_warning():
     msg = (
         "To align optimagic with scipy.optimize, the `derivative` argument has been "
         "renamed to `jac`. Please use `jac` instead of `derivative`. Using `derivative`"
-        " will become an error in optimagic version 0.6.0 and later."
+        " will become an error in optimagic version 0.6.0 and later. For more details "
+        "see the documentation: "
+        "https://optimagic.readthedocs.io/en/latest/how_to/how_to_derivatives.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -55,7 +57,8 @@ def throw_derivative_kwargs_future_warning():
         "To align optimagic with scipy.optimize, the `derivative_kwargs` argument has "
         "been renamed to `jac_kwargs`. Please use `jac_kwargs` instead of "
         "`derivative_kwargs`. Using `derivative_kwargs` will become an error in "
-        "optimagic version 0.6.0 and later."
+        "optimagic version 0.6.0 and later. For more details see the documentation: "
+        "https://optimagic.readthedocs.io/en/latest/how_to/how_to_derivatives.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -65,7 +68,9 @@ def throw_criterion_and_derivative_future_warning():
         "To align optimagic with scipy.optimize, the `criterion_and_derivative` "
         "argument has been renamed to `fun_and_jac`. Please use `fun_and_jac` "
         "instead of `criterion_and_derivative`. Using `criterion_and_derivative` "
-        "will become an error in optimagic version 0.6.0 and later."
+        "will become an error in optimagic version 0.6.0 and later. For more details "
+        "see the documentation: "
+        "https://optimagic.readthedocs.io/en/latest/how_to/how_to_derivatives.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -76,7 +81,8 @@ def throw_criterion_and_derivative_kwargs_future_warning():
         "argument has been renamed to `fun_and_jac_kwargs`. Please use "
         "`fun_and_jac_kwargs` instead of `criterion_and_derivative_kwargs`. Using "
         "`criterion_and_derivative_kwargs` will become an error in optimagic version "
-        "0.6.0 and later."
+        "0.6.0 and later. For more details see the documentation: "
+        "https://optimagic.readthedocs.io/en/latest/how_to/how_to_derivatives.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -94,7 +100,9 @@ def throw_multistart_options_future_warning():
     msg = (
         "Specifying multistart options via the argument `multistart_options` is "
         "deprecated and will be removed in optimagic version 0.6.0 and later. You can "
-        "pass these options directly to the `multistart` argument instead."
+        "pass these options directly to the `multistart` argument instead. For more "
+        "details see the documentation: "
+        "https://optimagic.readthedocs.io/en/latest/how_to/how_to_multistart.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -279,7 +287,8 @@ def throw_dict_output_warning():
         "0.6.0 and later. Please use the optimagic.mark.scalar, optimagic.mark."
         "least_squares, or optimagic.mark.likelihood decorators to indicate the type "
         "of problem you are solving. Use optimagic.FunctionValue objects to return "
-        "additional information for the logging."
+        "additional information for the logging. Please see the documentation for more "
+        "details: https://optimagic.readthedocs.io/en/latest/how_to/how_to_criterion_function.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -367,6 +376,10 @@ def throw_dict_constraints_future_warning_if_required(
         )
         for t in types:
             msg += f"  {{'type': '{t}', ...}} -> {replacements[t]}(...)\n"
+        msg += (
+            "\nFor more details see the documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_constraints.html"
+        )
 
         warnings.warn(msg, FutureWarning)
 
@@ -387,14 +400,17 @@ def replace_and_warn_about_deprecated_multistart_options(options):
         msg = (
             "The `share_optimization` option is deprecated and will be removed in "
             "version 0.6.0. Use `stopping_maxopt` instead to specify the number of "
-            "optimizations directly."
+            "optimizations directly. For more details see the documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_multistart.html"
         )
         warnings.warn(msg, FutureWarning)
 
     if options.convergence_relative_params_tolerance is not None:
         msg = (
             "The `convergence_relative_params_tolerance` option is deprecated and will "
-            "be removed in version 0.6.0. Use `convergence_xtol_rel` instead."
+            "be removed in version 0.6.0. Use `convergence_xtol_rel` instead. For more "
+            "details see the documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_convergence.html"
         )
         warnings.warn(msg, FutureWarning)
         if options.convergence_xtol_rel is None:
@@ -407,7 +423,9 @@ def replace_and_warn_about_deprecated_multistart_options(options):
             "The `optimization_error_handling` option is deprecated and will be "
             "removed in version 0.6.0. Setting this attribute also sets the error "
             "handling for exploration. Use the new `error_handling` option to set the "
-            "error handling for both optimization and exploration."
+            "error handling for both optimization and exploration. For more details "
+            "see the documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_error_handling.html"
         )
         warnings.warn(msg, FutureWarning)
         if options.error_handling is None:
@@ -418,7 +436,9 @@ def replace_and_warn_about_deprecated_multistart_options(options):
             "The `exploration_error_handling` option is deprecated and will be "
             "removed in version 0.6.0. Setting this attribute also sets the error "
             "handling for exploration. Use the new `error_handling` option to set the "
-            "error handling for both optimization and exploration."
+            "error handling for both optimization and exploration. For more details "
+            "see the documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_error_handling.html"
         )
         warnings.warn(msg, FutureWarning)
         if options.error_handling is None:
@@ -435,7 +455,9 @@ def replace_and_warn_about_deprecated_base_steps(
         msg = (
             "The `base_steps` argument is deprecated and will be removed alongside "
             "Richardson extrapolation in optimagic version 0.6.0. To specify the "
-            "step size use the `step_size` argument instead."
+            "step size use the `step_size` argument instead. For more details see the "
+            "documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_step_size.html"
         )
         warnings.warn(msg, FutureWarning)
 
@@ -448,10 +470,11 @@ def replace_and_warn_about_deprecated_base_steps(
 def replace_and_warn_about_deprecated_derivatives(candidate, name):
     msg = (
         f"Specifying a dictionary of {name} functions is deprecated and will be "
-        "removed in optimagic version 0.6.0. Please specify a single function that has "
+        "removed in optimagic version 0.6.0. Please specify a single function that "
         "returns the correct derivative for your optimizer or a list of functions that "
         "are decorated with the `mark.scalar`, `mark.likelihood` or "
-        "`mark.least_squares` decorators."
+        "`mark.least_squares` decorators. For more details see the documentation: "
+        "https://optimagic.readthedocs.io/en/latest/how_to/how_to_derivatives.html"
     )
     warnings.warn(msg, FutureWarning)
 
@@ -552,7 +575,9 @@ def pre_process_constraints(
     else:
         msg = (
             f"Invalid constraint type: {type(constraints)}. Must be a constraint "
-            "object or list thereof imported from `optimagic`."
+            "object or list thereof imported from `optimagic`. For more details see "
+            "the documentation: "
+            "https://optimagic.readthedocs.io/en/latest/how_to/how_to_constraints.html"
         )
         raise InvalidConstraintError(msg)
 

diff --git a/src/optimagic/optimization/create_optimization_problem.py b/src/optimagic/optimization/create_optimization_problem.py
@@ -282,23 +282,23 @@ def create_optimization_problem(
     if hess is not None:
         msg = (
             "The hess argument is not yet supported in optimagic. Creat an issue on "
-            "https://github.com/OpenSourceEconomics/optimagic/ if you have urgent need "
+            "https://github.com/optimagic-dev/optimagic/ if you have urgent need "
             "for this feature."
         )
         raise NotImplementedError(msg)
 
     if hessp is not None:
         msg = (
             "The hessp argument is not yet supported in optimagic. Creat an issue on "
-            "https://github.com/OpenSourceEconomics/optimagic/ if you have urgent need "
+            "https://github.com/optimagic-dev/optimagic/ if you have urgent need "
             "for this feature."
         )
         raise NotImplementedError(msg)
 
     if callback is not None:
         msg = (
             "The callback argument is not yet supported in optimagic. Creat an issue "
-            "on https://github.com/OpenSourceEconomics/optimagic/ if you have urgent "
+            "on https://github.com/optimagic-dev/optimagic/ if you have urgent "
             "need for this feature."
         )
         raise NotImplementedError(msg)