Finish pyproject.toml migration (#382)

* Gather system `import`s and separate from external

* Reorder external `import`s

* Run `import setuptools`

* Use `setuptools` instead of `distutils`

* Drop explicit `cythonize` calls

As `setuptools` will handle this for us, go ahead and drop the
`cythonize` calls.

* Use Cython's `build_ext` (if available)

* Drop `setup_requires`

Since these build requirements are already in `pyproject.toml` and that
is the preferred way forward, drop them from `setup.py`.

* Move setuptool-scm config to `pyproject.toml`

* Move nearly all of `setup.py` to `pyproject.toml`

* Add more URLs

* Add `.txt` extension to license

* Use latest setuptools build backend

* Drop extra whitespace

* Add release note

* Fix lint

* Move `pytest` config options to `pyproject.toml`

* Move `.coveragerc` into `pyproject.toml`

* Standardize on `setuptools-scm` with `-`

* Add `setuptools` & `setuptools-scm` to dev reqs

* Consolidate requirements

* Move `setuptools` after `project` items

* Simplify classifiers

* Drop doc build as it already happens on RTD

This preceeded docs builds on RTD for PRs. Now that RTD does PR builds
for docs, this is redundant. So drop it.

* Move `msgpack` later and unwrap

* Run `flake8` before tests

* Bake coverage & doctest flags into pytest config

* Drop `coveralls` from dependencies

* Fix Codecov release note reference

* Use `int16` in doctests for consistent reprs

Windows defaults to `int32` so won't display those `dtype`s. Whereas
UNIX defaults to `int64` and so won't display those `dtype`s. This
creates mismatches between the representations in docstrings between the
two platforms. For simplicity just use `int16`, which both platforms
will represent the same. This should ensure consistency with doctests.

* Add coverage report output type to config too

* Push `numcodecs` test path into config

* Exclude directories outside of numcodecs

* Simplify `flake8` instructions

* Delete unused `build.cmd`

This was used to configure compilers on Windows in the past.
Particularly it was used to configure Python 2.7 Windows builds. However
as of Python 3.5 and UCRT on Windows, this is unnecessary. Further
Python 2.7 was improved by a one off Windows Python compiler installer.
In any event this can safely be dropped. It is not used in this repo and
shouldn't be needed outside of it.

* Drop upper bound on Python

* Drop `requirements_dev.txt` too

* Always use Cython's `new_build_ext`

This should always be available as `cython` is a build requirement. So
simplify to just use Cython and skip `setuptools` here.

Author: jakirkham

.coveragerc

@@ -1,2 +1,14 @@
 [flake8]
 max-line-length = 100
+exclude =
+    .git,
+    .github,
+    .pytest_cache,
+    adhoc,
+    build,
+    c-blosc,
+    dist,
+    docs,
+    fixture,
+    notebooks,
+    numcodecs.egg-info,

.flake8

@@ -24,23 +24,16 @@ jobs:
 
       - name: Install numcodecs
         run: |
-          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
-          python -m pip install -v -e .
+          python -m pip install -v -e .[test,msgpack,zfpy]
 
       - name: List installed packages
         run: python -m pip list
 
-      - name: Run tests
-        run: pytest -v --cov=numcodecs --cov-report xml --doctest-modules --doctest-glob=*.pyx numcodecs
-
       - name: Flake8
-        run: flake8 numcodecs
+        run: flake8
 
-      - name: Build Docs
-        run: |
-          pip install -r requirements_rtfd.txt
-          cd docs
-          sphinx-build -W -b html -d {envtmpdir}/doctrees . {envtmpdir}/html
+      - name: Run tests
+        run: pytest -v
 
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/ci-linux.yaml

@@ -37,7 +37,6 @@ jobs:
           conda create -n env python=${{matrix.python-version}} wheel pip compilers 'clang>=12.0.1'
           conda activate env
           which pip
-          pip install -r requirements_test.txt -r requirements.txt
           conda env export
 
       - name: Show info about `env` environment
@@ -50,14 +49,13 @@ jobs:
         run: |
           conda activate env
           export CC=clang
-          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
-          python -m pip install -v -e .
+          python -m pip install -v -e .[test,msgpack,zfpy]
 
       - name: Run tests
         shell: "bash -l {0}"
         run: |
           conda activate env
-          pytest -v --cov=numcodecs --cov-report xml numcodecs
+          pytest -v
 
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/ci-osx.yaml

@@ -30,22 +30,20 @@ jobs:
           conda create -n env python=${{matrix.python-version}} wheel pip compilers
           conda activate env
           which pip
-          pip install -r requirements_test.txt -r requirements.txt
           conda env export
 
       - name: Install numcodecs
         shell: "bash -l {0}"
         run: |
           conda activate env
           export CC=clang
-          python -m pip install -U pip -r requirements_test.txt -r requirements.txt
-          python -m pip install -v -e .
+          python -m pip install -v -e .[test,msgpack,zfpy]
 
       - name: Run tests
         shell: "bash -l {0}"
         run: |
           conda activate env
-          pytest -v --cov=numcodecs --cov-report xml numcodecs
+          pytest -v
 
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/ci-windows.yaml

@@ -2,17 +2,3 @@
 # see https://pyup.io/docs/configuration/ for all available options
 
 schedule: every month
-
-requirements:
-  - requirements.txt:
-      pin: False
-      update: False
-  - requirements_test.txt:
-      pin: False
-      update: False
-  - requirements_rtfd.txt:
-      pin: False
-      update: False
-  - requirements_dev.txt:
-      pin: True
-      update: all

.pyup.yml

@@ -13,6 +13,7 @@ sphinx:
 
 python:
   install:
-    - requirements: requirements_rtfd.txt
     - method: pip
       path: .
+      extra_requirements:
+        - docs

.readthedocs.yaml

@@ -99,16 +99,11 @@ the repository, you can do something like the following::
     $ mkdir -p ~/pyenv/numcodecs-dev
     $ virtualenv --no-site-packages --python=/usr/bin/python3.9 ~/pyenv/numcodecs-dev
     $ source ~/pyenv/numcodecs-dev/bin/activate
-    $ pip install -r requirements_dev.txt
-    $ python setup.py build_ext --inplace
+    $ pip install -e .[docs,test,msgpack,zfpy]
 
 To verify that your development environment is working, you can run the unit tests::
 
-    $ pytest -v numcodecs
-
-To install numcodecs globally in editable mode run::
-
-    $ python -m pip install -e . 
+    $ pytest -v
 
 Creating a branch
 ~~~~~~~~~~~~~~~~~
@@ -147,11 +142,7 @@ Running the test suite
 NumCodecs includes a suite of unit tests, as well as doctests included in function and class
 docstrings. The simplest way to run the unit tests is to invoke::
 
-    $ pytest -v numcodecs
-
-To also run the doctests within docstrings, run::
-
-    $ pytest -v --doctest-modules numcodecs
+    $ pytest -v
 
 NumCodecs currently supports Python 6-3.9, so the above command must
 succeed before code can be accepted into the main code base.
@@ -167,14 +158,14 @@ All code must conform to the PEP8 standard. Regarding line length, lines up to 1
 characters are allowed, although please try to keep under 90 wherever possible.
 Conformance can be checked by running::
 
-    $ flake8 --max-line-length=100 numcodecs
+    $ flake8
 
 Test coverage
 ~~~~~~~~~~~~~
 
 NumCodecs maintains 100% test coverage under the latest Python stable release (currently
 Python 3.9). Both unit tests and docstring doctests are included when computing
-coverage. Running ``pytest -v --cov=numcodecs`` will automatically run the test suite with coverage
+coverage. Running ``pytest -v`` will automatically run the test suite with coverage
 and produce a coverage report. This should be 100% before code can be accepted into the
 main code base.