Convert setup.cfg to pyproject.toml (PlasmaPy#1758)

Co-authored-by: Nick Murphy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Closes PlasmaPy#1680 Closes PlasmaPy#1276
MKastek · Dec 13, 2022 · f5ff8e6 · f5ff8e6
1 parent b11560f
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diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -73,10 +73,11 @@ jobs:
           python: 3.8
           toxenv: py38-all
 
-        - name: Python 3.9
+        - name: Python 3.9, develop mode
           os: ubuntu-latest
           python: 3.9
           toxenv: py39
+          toxargs: --develop
 
     steps:
     - name: Checkout code
@@ -180,16 +181,14 @@ jobs:
         python-version: 3.8
     - name: Install requirements
       run: |
-        pip install --progress-bar off --upgrade pip
-        pip install --progress-bar off setuptools numpy wheel setuptools_scm twine
-    - name: Build a binary wheel
-      run: python setup.py bdist_wheel
+        pip install --progress-bar off setuptools numpy wheel setuptools_scm twine build pip
     - name: Build a source tarball
-      run: python setup.py sdist
+      run: python -m build --sdist --outdir dist/
+    - name: Build a binary wheel
+      run: python -m build --wheel --outdir dist/
     - name: Twine check
       run: twine check dist/*
     - name: Install PlasmaPy in all variants
       run: |
-        pip install --progress-bar off .[all,dev]
-        pip install --progress-bar off -e .[all,dev]
-        python setup.py develop
+        pip install --progress-bar off .[dev]
+        pip install --progress-bar off -e .[dev]
diff --git a/.gitignore b/.gitignore
@@ -137,7 +137,6 @@ untitled*
 auto_examples
 
 # Version file
-plasmapy/version.py
 plasmapy/_version.py
 tags
 docs/notebooks/*.md
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -8,12 +8,20 @@ version: 2
 formats:
 - htmlzip
 
+build:
+  os: ubuntu-20.04
+  tools:
+    python: '3.10'
+  jobs:
+    pre_create_environment:
+    - python -m pip install --upgrade setuptools pip
+
+
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: '3.8'
   install:
-  - requirements: requirements/install.txt
-  - requirements: requirements/docs.txt
-  - method: setuptools
+  - method: pip
     path: .
+    extra_requirements:
+    - docs
   system_packages: true
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,16 +1,17 @@
 include README.md
 include LICENSE.md
-include setup.py
 include pyproject.toml
 
-include setup.cfg
 include plasmapy/tests/coveragerc
 include CITATION.cff
 
 recursive-include plasmapy *.json *.npy
 recursive-include docs *
 recursive-include licenses *
 
+# Only for editable installs
+prune plasmapy/_dev
+
 prune build
 prune docs/_build
 prune docs/api

diff --git a/binder/requirements.txt b/binder/requirements.txt
@@ -1,5 +1,3 @@
--r ../requirements/build.txt
--r ../requirements/install.txt
--r ../requirements/extras.txt
 .
+..
 jupytext
diff --git a/changelog/1758.trivial.rst b/changelog/1758.trivial.rst
@@ -0,0 +1,3 @@
+Transferred most of the contents of :file:`setup.py` and :file:`setup.cfg` to
+|pyproject.toml|_ (see :pep:`518` and :pep:`621`). Simplified ``extras``
+requirements (``pip install plasmapy[all]`` and ``[extras]`` are gone).
diff --git a/changelog/README.rst b/changelog/README.rst
@@ -164,7 +164,7 @@ to the top-level directory of your local clone of PlasmaPy and run:
 
 .. code-block:: shell
 
-   pip install -r requirements.txt
+   pip install -e .[dev]
 
 Configuration files for towncrier_ are in :file:`pyproject.toml`.
 

diff --git a/docs/common_links.rst b/docs/common_links.rst
@@ -260,18 +260,6 @@
 .. _`pyproject.toml`: https://github.com/PlasmaPy/PlasmaPy/blob/main/pyproject.toml
 .. |pyproject.toml| replace:: :file:`pyproject.toml`
 
-.. _`requirements`: https://github.com/PlasmaPy/PlasmaPy/tree/main/requirements
-.. |requirements| replace:: :file:`requirements`
-
-.. _`requirements/build.txt`: https://github.com/PlasmaPy/PlasmaPy/blob/main/requirements/build.txt
-.. |requirements/build.txt| replace:: :file:`requirements/build.txt`
-
-.. _`requirements/environment.yml`: https://github.com/PlasmaPy/PlasmaPy/blob/main/requirements/environment.yml
-.. |requirements/environment.yml| replace:: :file:`requirements/environment.yml`
-
-.. _`setup.cfg`: https://github.com/PlasmaPy/PlasmaPy/blob/main/setup.cfg
-.. |setup.cfg| replace:: :file:`setup.cfg`
-
 .. _`sphinxcontrib-bibtex`: https://sphinxcontrib-bibtex.readthedocs.io
 .. |sphinxcontrib-bibtex| replace:: `sphinxcontrib-bibtex`
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -314,7 +314,7 @@
 # a new role, and the corresponding tuple contains the base url and the
 # caption. For example, we can now do :orcid:`0000-0000-0000-0000` and
 # have a link create to the corresponding ORCID page. New roles should
-# be added to rst-roles in setup.cfg to avoid being caught by
+# be added to rst-roles in tox.ini to avoid being caught by
 # flake8-rst-docstrings.
 
 extlinks = {

diff --git a/docs/contributing/coding_guide.rst b/docs/contributing/coding_guide.rst
@@ -305,26 +305,8 @@ Imports
 Requirements
 ============
 
-* Package requirements are specified in multiple locations that need to
-  be updated simultaneously.
-
-  - The |requirements|_ directory contains multiple text files that
-    contain build, installation, testing, documentation, and extra
-    requirements.
-
-  - The ``build-system.requires`` section of |pyproject.toml|_ includes
-    the requirements for building PlasmaPy. This section must mirror
-    |requirements/build.txt|_.
-
-  - |setup.cfg|_ includes sections for the install, docs, tests, and
-    extra requirements that must mirror the corresponding files in
-    the |requirements|_ directory.
-
-  - |requirements/environment.yml|_ contains a Conda_ environment
-    for PlasmaPy.
-
-  - |tox.ini|_ contains a testing environment for the minimal
-    dependencies.
+* Package requirements are specified in |pyproject.toml|_. |tox.ini|_
+  also contains a testing environment for the minimal dependencies.
 
 * Each release of PlasmaPy should support all minor versions of
   Python that have been released in the prior 42 months, and all minor

diff --git a/docs/contributing/doc_guide.rst b/docs/contributing/doc_guide.rst
@@ -77,7 +77,7 @@ and run:
 
 .. code-block:: bash
 
-   pip install -r requirements.txt
+   pip install -e .[dev]
 
 It may also be necessary to install the following software:
 
@@ -395,7 +395,7 @@ value in |docs/conf.py|_.
 
 When an extension contains new |roles| or |directives|, it may be
 necessary to add them to ``rst-roles`` and ``rst-directives`` in the
-``[flake8]`` section of |setup.cfg|_ to avoid linter errors during
+``[flake8]`` section of |tox.ini|_ to avoid linter errors during
 continuous integration tests in pull requests.
 
 .. _external-references:

diff --git a/docs/contributing/install_dev.rst b/docs/contributing/install_dev.rst
@@ -103,7 +103,7 @@ following:
 
 .. code-block:: bash
 
-   conda env create -f requirements/environment.yml
+   conda create -n plasmapy python=3.10
 
 You may now enter the environment via
 
@@ -171,7 +171,7 @@ dependencies. One way to do this is to do
 
 Next, setup the development version of PlasmaPy which you just cloned
 by moving into the root directory of the cloned repo and running the
-setup.py script there:
+following there:
 
 .. code-block:: bash
 
@@ -204,11 +204,10 @@ Installing your own dev version
 ===============================
 
 To be able to import PlasmaPy from your source version, enter the
-repository root and use one of
+repository root and use
 
 .. code-block:: bash
 
-   python setup.py develop
    pip install -e .
 
 .. note::

diff --git a/docs/contributing/testing_guide.rst b/docs/contributing/testing_guide.rst
@@ -175,7 +175,7 @@ The following checks are performed with each pull request.
 
   * Occasionally codespell_ will report false positives. Please add
     false positives to ``ignore-words-list`` under ``codespell`` in
-    :file:`setup.cfg`.
+    :file:`pyproject.toml`.
 
 .. note::
 
@@ -200,7 +200,7 @@ To install the packages necessary to run tests on your local computer
 
 .. code-block:: shell
 
-   pip install -r requirements.txt
+   pip install -e .[tests]
 
 To run PlasmaPy's tests from the command line, go to a directory within
 PlasmaPy's repository and run:

diff --git a/docs/install.rst b/docs/install.rst
@@ -194,9 +194,9 @@ If you expect to occasionally edit the source code, instead run:
 
 .. code:: bash
 
-   pip install -e .[developer]
+   pip install -e ".[dev]"
 
-The ``-e`` flag makes the installation editable and ``[developer]``
+The ``-e`` flag makes the installation editable and ``[dev]``
 indicates that all of the dependencies needed for developing PlasmaPy
 will be installed.
 

diff --git a/plasmapy/__init__.py b/plasmapy/__init__.py
@@ -28,7 +28,7 @@
 # Packages may add whatever they like to this file, but
 # should keep this content at the top.
 # ----------------------------------------------------------------------------
-from importlib.metadata import PackageNotFoundError, version
+from importlib.metadata import PackageNotFoundError
 
 from plasmapy import (
     analysis,
@@ -43,46 +43,22 @@
 
 # define version
 try:
-    # this places a runtime dependency on setuptools
-    #
-    # note: if there's any distribution metadata in your source files, then this
-    #       will find a version based on those files.  Keep distribution metadata
-    #       out of your repository unless you've intentionally installed the package
-    #       as editable (e.g. `pip install -e {plasmapy_directory_root}`),
-    #       but then __version__ will not be updated with each commit, it is
-    #       frozen to the version at time of install.
-    #
-    #: PlasmaPy version string
-    __version__ = version("plasmapy")
-except PackageNotFoundError:
-    # package is not installed
-    fallback_version = "unknown"
     try:
-        # code most likely being used from source
-        # if setuptools_scm is installed then generate a version
-        from setuptools_scm import get_version
-
-        __version__ = get_version(
-            root="..", relative_to=__file__, fallback_version=fallback_version
-        )
-        del get_version
-        warn_add = "setuptools_scm failed to detect the version"
-    except ModuleNotFoundError:
-        # setuptools_scm is not installed
-        __version__ = fallback_version
-        warn_add = "setuptools_scm is not installed"
-
-    if __version__ == fallback_version:
-        from warnings import warn
-
-        warn(
-            f"plasmapy.__version__ not generated (set to 'unknown'), PlasmaPy is "
-            f"not an installed package and {warn_add}.",
-            RuntimeWarning,
-        )
-
-        del warn
-    del fallback_version, warn_add
+        from plasmapy._dev.scm_version import version as __version__
+    except ImportError:
+        from plasmapy._version import version as __version__
+except Exception:  # coverage: ignore
+    # package is not installed
+    __version__ = "0.0.0"
+
+    from warnings import warn
+
+    warn(
+        "plasmapy.__version__ not generated (set to '0.0.0'). It looks like "
+        "the installation's broken. Ask on Element!",
+    )
+
+    del warn
 
 # ----------------------------------------------------------------------------
 #: PlasmaPy citation instructions
@@ -92,7 +68,7 @@
 )
 
 
-def online_help(query: str):
+def online_help(query: str):  # coverage: ignore
     """
     Open a webpage containing a search page in `PlasmaPy's documentation`_,
     or another page that contains relevant online help.

diff --git a/plasmapy/_dev/__init__.py b/plasmapy/_dev/__init__.py
@@ -0,0 +1,8 @@
+"""
+This subpackage is only used with an editable install of PlasmaPy.
+
+It ensures that setuptools-scm gets the right version. This is helpful,
+for example, with documentation builds.
+
+Its implementation follows the setup of https://github.com/astropy/astropy/pull/10774.
+"""
diff --git a/plasmapy/_dev/scm_version.py b/plasmapy/_dev/scm_version.py
@@ -0,0 +1,10 @@
+# Try to use setuptools_scm to get the current version; this is only used
+# in development installations from the git repository.
+import os.path as pth
+
+try:
+    from setuptools_scm import get_version
+
+    version = get_version(root=pth.join("..", ".."), relative_to=__file__)
+except Exception as e:
+    raise ImportError("setuptools_scm broken or not installed") from e