NEP29: Set minimum required versions to NumPy 1.17+ and Python 3.7+ (#1074)

Start adopting NEP29 - Recommend Python and NumPy
version support as a community policy standard, see
https://numpy.org/neps/nep-0029-deprecation_policy.html.
Bumps minimum supported NumPy version to 1.17 in the
setup.py, requirements.txt and environment.yml files. Also
set minimum required Python version to be 3.7+.

* Modify CI test matrix to test on Numpy 1.17 and 1.20, Python 3.7 and 3.9

Test only on minimum and maximum supported versions
according to NEP. I.e. minimum of NumPy 1.17 and Py3.7,
maximum of NumPy 1.20 and Py3.9. This drops testing on
the middle Python 3.8 version to conserve CI resources.

* Add NumPy version to codecov reporting
* Update website links of PyGMT deps to use https and official sources
* Update MAINTENANCE.md to mention two Linux CI jobs are run in draft PRs
* Place NEP29 dependencies policy in MAINTENANCE.md
* List NumPy in compatibility version list on main README.rst page

Author: weiji14

.github/workflows/ci_tests.yaml

@@ -25,12 +25,12 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9]
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -41,20 +41,24 @@ jobs:
             isDraft: true
           - os: windows-latest
             isDraft: true
-          - os: ubuntu-latest
-            python-version: 3.7
-            isDraft: true
-          - os: ubuntu-latest
-            python-version: 3.8
-            isDraft: true
+          # - os: ubuntu-latest
+          #   python-version: 3.7
+          #   isDraft: true
+        # Pair Python 3.7 with NumPy 1.17 and Python 3.9 with NumPy 1.20
+        include:
+          - python-version: 3.7
+            numpy-version: '1.17'
+          - python-version: 3.9
+            numpy-version: '1.20'
     defaults:
       run:
         shell: bash -l {0}
 
-    # environmental variables used in coverage
+    # Environment variables used by codecov
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
+      NUMPY: ${{ matrix.numpy-version }}
 
     steps:
       # Cancel previous runs that are not completed
@@ -82,7 +86,8 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
+          conda install gmt=6.1.1 numpy=${{ matrix.numpy-version }} \
+                        pandas xarray netCDF4 packaging \
                         codecov coverage[toml] dvc ipython make \
                         pytest-cov pytest-mpl pytest>=6.0 \
                         sphinx-gallery
@@ -138,5 +143,5 @@ jobs:
         uses: codecov/[email protected]
         with:
           file: ./coverage.xml # optional
-          env_vars: OS,PYTHON
+          env_vars: OS,PYTHON,NUMPY
           fail_ci_if_error: false

MAINTENANCE.md

@@ -12,6 +12,7 @@ If you want to make a contribution to the project, see the
 * [Reviewing and Merging Pull Requests](#reviewing-and-merging-pull-requests)
 * [Continuous Integration](#continuous-integration)
 * [Continuous Documentation](#continuous-documentation)
+* [Dependencies Policy](#dependencies-policy)
 * [Making a Release](#making-a-release)
     - [Updating the Changelog](#updating-the-changelog)
     - [Check the README Syntax](#check-the-readme-syntax)
@@ -77,8 +78,9 @@ There are 9 configuration files located in `.github/workflows`:
 
    This is run on every commit to the *master* and Pull Request branches.
    It is also scheduled to run daily on the *master* branch.
-   In draft Pull Requests, only one job (Linux + Python latest)
-   is triggered to save on Continuous Integration resources.
+   In draft Pull Requests, only two jobs on Linux (minimum NEP29 Python/NumPy versions
+   and latest Python/NumPy versions) are triggered to save on Continuous Integration
+   resources.
 
 3. `ci_docs.yml` (Build documentation on Linux/macOS/Windows)
 
@@ -135,6 +137,22 @@ The actual script `package.json` is used by Vercel to install the necessary pack
 build the documentation, copy the files to a 'public' folder and deploy that to the web,
 see https://vercel.com/docs/build-step.
 
+
+## Dependencies Policy
+
+PyGMT has adopted [NEP29](https://numpy.org/neps/nep-0029-deprecation_policy)
+alongside the rest of the Scientific Python ecosystem, and therefore supports:
+
+* All minor versions of Python released 42 months prior to the project,
+  and at minimum the two latest minor versions.
+* All minor versions of NumPy released in the 24 months prior to the project,
+  and at minimum the last three minor versions.
+
+In `setup.py`, the `python_requires` variable should be set to the minimum
+supported version of Python. Minimum Python and NumPy version support should be
+adjusted upward on every major and minor release, but never on a patch release.
+
+
 ## Making a Release
 
 We try to automate the release process as much as possible.

README.rst

@@ -229,14 +229,15 @@ Documentation for other versions
 * `v0.1.0 <https://www.pygmt.org/v0.1.0>`__
 * `v0.0.1a0 <https://www.pygmt.org/0.0.1a0>`__
 
-Compatibility with Python and GMT versions
-------------------------------------------
+Compatibility with GMT and Python/NumPy versions
+------------------------------------------------
 
-======= ========== =========
-PyGMT   GMT        Python
-======= ========== =========
+======= ========== ========= =========
+PyGMT   GMT        Python    NumPy
+======= ========== ========= =========
+0.4.x   >=6.2.0    >=3.7     >=1.17.0
 0.3.x   >=6.1.1    >=3.7
 0.2.1   >=6.1.1    >=3.6
 0.2.0   >=6.1.1    3.6 - 3.8
 0.1.x   >=6.0.0    3.6 - 3.8
-======= ========== =========
+======= ========== ========= =========

doc/install.rst

@@ -46,8 +46,7 @@ Start by looking at the tutorials on our sidebar, good luck!
 Which Python?
 -------------
 
-PyGMT is tested to run on **Python 3.7 or greater**. Older Python versions may
-work, but there is no guarantee that PyGMT will behave as expected.
+PyGMT is tested to run on **Python 3.7 or greater**.
 
 We recommend using the `Anaconda <https://www.anaconda.com/distribution>`__
 Python distribution to ensure you have all dependencies installed and the
@@ -79,19 +78,17 @@ We recommend following the instructions further on to install GMT 6.
 Dependencies
 ------------
 
-PyGMT requires the following libraries:
+PyGMT requires the following libraries to be installed:
 
-* `numpy <http://www.numpy.org/>`__
-* `pandas <https://pandas.pydata.org/>`__
-* `xarray <http://xarray.pydata.org/>`__
-* `netCDF4 <https://github.com/Unidata/netcdf4-python>`__
-* `packaging <https://pypi.org/project/packaging/>`__
+* `numpy <https://numpy.org>`__ (>= 1.17)
+* `pandas <https://pandas.pydata.org>`__
+* `xarray <https://xarray.pydata.org>`__
+* `netCDF4 <https://unidata.github.io/netcdf4-python>`__
+* `packaging <https://packaging.pypa.io>`__
 
 The following are optional (but recommended) dependencies:
 
-* `IPython <https://ipython.org/>`__: For embedding the figures in Jupyter
-  notebooks.
-
+* `IPython <https://ipython.org>`__: For embedding the figures in Jupyter notebooks.
 
 Installing GMT and other dependencies
 -------------------------------------

environment.yml

@@ -6,7 +6,7 @@ dependencies:
     # Required dependencies
     - pip
     - gmt=6.1.1
-    - numpy
+    - numpy>=1.17
     - pandas
     - xarray
     - netCDF4

requirements.txt

@@ -1,5 +1,5 @@
 # Required packages
-numpy
+numpy>=1.17
 pandas
 xarray
 netCDF4

setup.py

@@ -30,10 +30,11 @@
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
-    "License :: OSI Approved :: {}".format(LICENSE),
+    f"License :: OSI Approved :: {LICENSE}",
 ]
 PLATFORMS = "Any"
-INSTALL_REQUIRES = ["numpy", "pandas", "xarray", "netCDF4", "packaging"]
+PYTHON_REQUIRES = ">=3.7"
+INSTALL_REQUIRES = ["numpy>=1.17", "pandas", "xarray", "netCDF4", "packaging"]
 # Configuration for setuptools-scm
 SETUP_REQUIRES = ["setuptools_scm"]
 USE_SCM_VERSION = {"local_scheme": "node-and-date", "fallback_version": "unknown"}
@@ -57,6 +58,7 @@
         package_data=PACKAGE_DATA,
         classifiers=CLASSIFIERS,
         keywords=KEYWORDS,
+        python_requires=PYTHON_REQUIRES,
         install_requires=INSTALL_REQUIRES,
         setup_requires=SETUP_REQUIRES,
     )