Merge pull request #1114 from Ouranosinc/fix_setup_recipe

Fix upstream installation recipe for PyPI-compliance

.github/workflows/bump-version.yml

@@ -6,10 +6,16 @@ on:
       - master
     paths-ignore:
       - HISTORY.rst
+      - Makefile
+      - MANIFEST.in
+      - requirements_upstream.txt
       - setup.cfg
       - setup.py
       - tox.ini
       - xclim/__init__.py
+      - docs/**.ipynb
+      - docs/*.py
+      - docs/*.rst
       - .github/**.yml
       - .pre-commit-config.yaml
 

.github/workflows/codeql-analysis.yml

@@ -6,10 +6,16 @@ on:
       - master
     paths-ignore:
       - HISTORY.rst
+      - Makefile
+      - MANIFEST.in
+      - requirements_upstream.txt
       - setup.cfg
       - setup.py
       - tox.ini
       - xclim/__init__.py
+      - docs/**.ipynb
+      - docs/**.py
+      - docs/**.rst
       - .github/**.yml
       - .pre-commit-config.yaml
   schedule:

HISTORY.rst

@@ -25,7 +25,6 @@ New features and enhancements
 * Improved percentile based indicators metadata with the window, threshold and climatology period used to compute percentiles. (:issue:`1047`, :pull:`1050`).
 * New ``xclim.core.calendar.construct_offset``, the inverse operation of ``parse_offset``. (:pull:`1090`).
 * Rechunking operations in ``xclim.indices.run_length.rle`` are now synchronized with dask's options. (:pull:`1090`).
-* A convenience recipe for installing key development branches of some dependencies has been added (`$ pip install xclim[upstream]`). (:issue:`1088`, :pull:`1092`).
 * A mention of the "missing" checks and options is added to the history attribute of indicators, where appropriate. (:issue:`1100`, :pull:`1103`).
 
 Breaking changes
@@ -53,6 +52,8 @@ Internal changes
 * Test coverage statistic no longer includes coverage of the test files themselves. Coverage now reflects lines of usable code covered. (:pull:`1101`).
 * Reordered listed authors alphabetically. Promoted :user:`bzah` to core contributor. (:pull:`1105`).
 * Tests have been added for some functions in `xclim.testing.utils.py`; some previously uncaught bugs in ``list_input_variables``, ``publish_release_notes``, and ``show_versions`` have been patched. (:issue:`1078`, :pull:`1107`).
+* A convenience command for installing xclim with key development branches of some dependencies has been added (`$ make upstream`). (:issue:`1088`, :pull:`1092`; amended in :issue:`1113`, :pull:`1114`).
+    - This build configuration is also available in `tox` for local development purposes (`$ tox -e pyXX-upstream`).
 
 Bug fixes
 ^^^^^^^^^

MANIFEST.in

@@ -4,6 +4,7 @@ include HISTORY.rst
 include LICENSE
 include README.rst
 include requirements_dev.txt
+include requirements_upstream.txt
 
 recursive-include xclim *.txt *.json *.yml *.py
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

Makefile

@@ -106,3 +106,6 @@ install: clean ## install the package to the active Python's site-packages
 
 develop: clean ## install the package and development dependencies in editable mode to the active Python's site-packages
 	python -m pip install --no-user --editable ".[dev]"
+
+upstream: clean develop ## install the GitHub-based development branches of dependencies in editable mode to the active Python's site-packages
+	python -m pip install --no-user --requirement requirements_upstream.txt

docs/installation.rst

@@ -43,7 +43,9 @@ For convenience, these libraries can be installed alongside `xclim` using the fo
 
 .. code-block::
 
-    $ pip install -e ".[upstream]"
+    $ pip install -r requirements_upstream.txt
+    # Or, alternatively:
+    $ make upstream
 
 .. _flox: https://github.com/dcherian/flox
 .. _clisops: https://github.com/roocs/clisops
@@ -93,4 +95,4 @@ To create a conda development environment including all xclim dependencies, ente
 
     $ conda create -n my_xclim_env python=3.8 --file=environment.yml
     $ conda activate my_xclim_env
-    (my_xclim_env) $ pip install .[dev]
+    (my_xclim_env) $ pip install ".[dev]"

requirements_upstream.txt

@@ -0,0 +1,4 @@
+git+https://github.com/pydata/bottleneck.git@master#egg=bottleneck
+git+https://github.com/Unidata/cftime.git@master#egg=cftime
+git+https://github.com/dcherian/flox.git@main#egg=flox
+git+https://github.com/pydata/xarray.git@main#egg=xarray

setup.py

@@ -54,14 +54,6 @@
     for dependency in dev.readlines():
         dev_requirements.append(dependency)
 
-upstream_requirements = [
-    "wheel",
-    "bottleneck @ git+https://github.com/pydata/bottleneck.git@master#egg=bottleneck",
-    "cftime @ git+https://github.com/Unidata/cftime.git@master#egg=cftime",
-    "flox @ git+https://github.com/dcherian/flox.git@main#egg=flox",
-    "xarray @ git+https://github.com/pydata/xarray.git@main#egg=xarray",
-]
-
 KEYWORDS = "xclim climate climatology netcdf gridded analysis"
 
 setup(
@@ -94,7 +86,7 @@
         [console_scripts]
         xclim=xclim.cli:cli
     """,
-    extras_require={"dev": dev_requirements, "upstream": upstream_requirements},
+    extras_require={"dev": dev_requirements},
     url=URL,
     version=VERSION,
     zip_safe=False,

tox.ini

@@ -39,11 +39,6 @@ commands =
     pytest --nbval docs/notebooks --durations=3
     pytest --rootdir xclim/testing/tests/ --xdoctest xclim --ignore=xclim/testing/tests/ --durations=3
 
-[testenv:upstream]
-extras =
-    upstream
-    dev
-
 [testenv]
 setenv =
     PYTEST_ADDOPTS = "--color=yes"
@@ -54,6 +49,7 @@ extras = dev
 deps =
     coverage: coveralls
     lm3: git+https://github.com/OpenHydrology/lmoments3.git@develop#egg=lmoments3
+    upstream: -rrequirements_upstream.txt
 install_command = python -m pip install --no-user {opts} {packages}
 download = True
 commands =