From 9b43e006d37827248bd9404fce9653ae081327fd Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 10:42:34 -0400 Subject: [PATCH 1/9] try testing 3.12 [1] --- .github/workflows/unittests.yml | 23 ++++++++++++++-------- ci/312-dev.yaml | 35 +++++++++++++++++++++++++++++++++ ci/312-no-optional.yaml | 21 ++++++++++++++++++++ ci/312.yaml | 27 +++++++++++++++++++++++++ 4 files changed, 98 insertions(+), 8 deletions(-) create mode 100644 ci/312-dev.yaml create mode 100644 ci/312-no-optional.yaml create mode 100644 ci/312.yaml diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml index 6c38276b2..b3ccf5779 100644 --- a/.github/workflows/unittests.yml +++ b/.github/workflows/unittests.yml @@ -18,16 +18,23 @@ jobs: matrix: os: [ubuntu-latest] environment-file: - - ci/38-minimal.yaml - - ci/39.yaml - - ci/310.yaml - - ci/311.yaml - - ci/311-dev.yaml - - ci/311-no-optional.yaml + #- ci/38-minimal.yaml + #- ci/39.yaml + #- ci/310.yaml + #- ci/311.yaml + #- ci/311-dev.yaml + #- ci/311-no-optional.yaml + - ci/312.yaml + - ci/312-dev.yaml + - ci/312-no-optional.yaml include: - - environment-file: ci/310.yaml + #- environment-file: ci/310.yaml + # os: macos-latest + #- environment-file: ci/310.yaml + # os: windows-latest + - environment-file: ci/312.yaml os: macos-latest - - environment-file: ci/310.yaml + - environment-file: ci/312.yaml os: windows-latest defaults: run: diff --git a/ci/312-dev.yaml b/ci/312-dev.yaml new file mode 100644 index 000000000..925d44563 --- /dev/null +++ b/ci/312-dev.yaml @@ -0,0 +1,35 @@ +name: test +channels: + - conda-forge +dependencies: + - python=3.12 + - platformdirs + - beautifulsoup4 + - jinja2 + # testing + - codecov + - matplotlib + - pytest + - pytest-cov + - pytest-xdist + # optional + - geos + - pyproj + - fiona + - joblib + - networkx + - packaging + - zstd + - Cython + - geodatasets + - pyarrow + - pip + - pip: + # dev versions of packages + - --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple + - scipy + - pandas + - xarray + - scikit-learn + - git+https://github.com/shapely/shapely.git@main + - git+https://github.com/geopandas/geopandas.git@main diff --git a/ci/312-no-optional.yaml b/ci/312-no-optional.yaml new file mode 100644 index 000000000..becf7bba7 --- /dev/null +++ b/ci/312-no-optional.yaml @@ -0,0 +1,21 @@ +name: test +channels: + - conda-forge +dependencies: + - python=3.12 + - platformdirs + - beautifulsoup4 + - jinja2 + - pandas + - scipy + - xarray + # testing + - codecov + - matplotlib + - pytest + - pytest-cov + - pytest-xdist + # optional used in ci + - geopandas-base>=0.12.0 # base to avoid pulling sklearn + - fiona + - geodatasets diff --git a/ci/312.yaml b/ci/312.yaml new file mode 100644 index 000000000..cefb868b0 --- /dev/null +++ b/ci/312.yaml @@ -0,0 +1,27 @@ +name: test +channels: + - conda-forge +dependencies: + - python=3.12 + - platformdirs + - beautifulsoup4 + - jinja2 + - pandas + - scipy + - xarray + # testing + - codecov + - matplotlib + - pytest + - pytest-cov + - pytest-xdist + # optional + - geopandas>=0.12.0 + - joblib + - networkx + - packaging + - shapely>=2.0b1 + - xarray + - zstd + - geodatasets + - pyarrow From 04c6025b65fcd9e9e4d041147fc280c6aa29181c Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 11:13:42 -0400 Subject: [PATCH 2/9] adjust repo for 3.10-3.12 support --- .github/workflows/unittests.yml | 13 ++------- .pre-commit-config.yaml | 2 +- README.rst | 6 ++-- ci/{38-minimal.yaml => 310-minimal.yaml} | 2 +- ci/311-dev.yaml | 35 ------------------------ ci/311-no-optional.yaml | 21 -------------- ci/39.yaml | 26 ------------------ docs/conf.py | 2 +- docs/index.rst | 10 +++---- pyproject.toml | 4 +-- 10 files changed, 16 insertions(+), 105 deletions(-) rename ci/{38-minimal.yaml => 310-minimal.yaml} (96%) delete mode 100644 ci/311-dev.yaml delete mode 100644 ci/311-no-optional.yaml delete mode 100644 ci/39.yaml diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml index d84df5fe7..a8b1bdc38 100644 --- a/.github/workflows/unittests.yml +++ b/.github/workflows/unittests.yml @@ -24,20 +24,13 @@ jobs: matrix: os: [ubuntu-latest] environment-file: - #- ci/38-minimal.yaml - #- ci/39.yaml - #- ci/310.yaml - #- ci/311.yaml - #- ci/311-dev.yaml - #- ci/311-no-optional.yaml + - ci/310-minimal.yaml + - ci/310.yaml + - ci/311.yaml - ci/312.yaml - ci/312-dev.yaml - ci/312-no-optional.yaml include: - #- environment-file: ci/310.yaml - # os: macos-latest - #- environment-file: ci/310.yaml - # os: windows-latest - environment-file: ci/312.yaml os: macos-latest - environment-file: ci/312.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 819dfc0e9..bef3987e3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/psf/black - rev: 23.9.1 + rev: "23.10.0" hooks: - id: black language_version: python3 diff --git a/README.rst b/README.rst index 8bf368875..12ad3f57f 100644 --- a/README.rst +++ b/README.rst @@ -5,7 +5,7 @@ Python Spatial Analysis Library Core .. image:: https://github.com/pysal/libpysal/workflows/.github/workflows/unittests.yml/badge.svg :target: https://github.com/pysal/libpysal/actions?query=workflow%3A.github%2Fworkflows%2Funittests.yml -.. image:: https://codecov.io/gh/pysal/libpysal/branch/master/graph/badge.svg +.. image:: https://codecov.io/gh/pysal/libpysal/branch/main/graph/badge.svg :target: https://codecov.io/gh/pysal/libpysal .. image:: https://badge.fury.io/py/libpysal.svg @@ -59,7 +59,7 @@ If you have any suggestions, feature requests, or bug reports, please open new `issues `_ on GitHub. To submit patches, please review `PySAL's documentation for developers `_, the PySAL `development guidelines `_, -the `libpysal contributing guidelines `_ +the `libpysal contributing guidelines `_ before opening a `pull request `_. Once your changes get merged, you’ll automatically be added to the `Contributors List `_. @@ -76,6 +76,6 @@ To search for or report bugs, please see `libpysal's issues `_ +See the `LICENSE `_ for information on the history of this software, terms & conditions for usage, and a DISCLAIMER OF ALL WARRANTIES. diff --git a/ci/38-minimal.yaml b/ci/310-minimal.yaml similarity index 96% rename from ci/38-minimal.yaml rename to ci/310-minimal.yaml index b0ecd5711..31dee52df 100644 --- a/ci/38-minimal.yaml +++ b/ci/310-minimal.yaml @@ -2,7 +2,7 @@ name: test channels: - conda-forge dependencies: - - python=3.8 + - python=3.10 - beautifulsoup4=4.10 - jinja2=3.0 - pandas=1.4 diff --git a/ci/311-dev.yaml b/ci/311-dev.yaml deleted file mode 100644 index e3e10d272..000000000 --- a/ci/311-dev.yaml +++ /dev/null @@ -1,35 +0,0 @@ -name: test -channels: - - conda-forge -dependencies: - - python=3.11 - - platformdirs - - beautifulsoup4 - - jinja2 - # testing - - codecov - - matplotlib - - pytest - - pytest-cov - - pytest-xdist - # optional - - geos - - pyproj - - fiona - - joblib - - networkx - - packaging - - zstd - - Cython - - geodatasets - - pyarrow - - pip - - pip: - # dev versions of packages - - --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple - - scipy - - pandas - - xarray - - scikit-learn - - git+https://github.com/shapely/shapely.git@main - - git+https://github.com/geopandas/geopandas.git@main diff --git a/ci/311-no-optional.yaml b/ci/311-no-optional.yaml deleted file mode 100644 index 1ffacef71..000000000 --- a/ci/311-no-optional.yaml +++ /dev/null @@ -1,21 +0,0 @@ -name: test -channels: - - conda-forge -dependencies: - - python=3.11 - - platformdirs - - beautifulsoup4 - - jinja2 - - pandas - - scipy - - xarray - # testing - - codecov - - matplotlib - - pytest - - pytest-cov - - pytest-xdist - # optional used in ci - - geopandas-base>=0.12.0 # base to avoid pulling sklearn - - fiona - - geodatasets diff --git a/ci/39.yaml b/ci/39.yaml deleted file mode 100644 index d9e0bb04f..000000000 --- a/ci/39.yaml +++ /dev/null @@ -1,26 +0,0 @@ -name: test -channels: - - conda-forge -dependencies: - - python=3.9 - - platformdirs - - beautifulsoup4 - - jinja2 - - pandas - - scipy - - xarray - # testing - - codecov - - matplotlib - - pytest - - pytest-cov - - pytest-xdist - # optional - - geopandas - - joblib - - networkx - - numba - - packaging - - zstd - - geodatasets - - pyarrow diff --git a/docs/conf.py b/docs/conf.py index 384dc552c..0c0208cbd 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -279,7 +279,7 @@ def setup(app): "networkx": ("https://networkx.org/documentation/stable/", None), "numpy": ("https://numpy.org/doc/stable/", None), "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), - "python": ("https://docs.python.org/3.11/", None), + "python": ("https://docs.python.org/3.12/", None), "scipy": ("https://docs.scipy.org/doc/scipy/", None), } diff --git a/docs/index.rst b/docs/index.rst index 8040ac2e3..bf71e97fb 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,7 +19,7 @@ libpysal: Python Spatial Analysis Library Core
- +
Weights for nonplanar enforced geometries
@@ -38,10 +38,10 @@ Introduction **libpysal** offers four modules that form the building blocks in many upstream packages in the `PySAL family `_: -- Spatial Weights: libpysal.weights -- Input-and output: libpysal.io -- Computational geometry: libpysal.cg -- Built-in example datasets libpysal.examples +- Spatial Weights: libpysal.weights +- Input-and output: libpysal.io +- Computational geometry: libpysal.cg +- Built-in example datasets libpysal.examples Examples demonstrating some of **libpysal** functionality are available in the `tutorial `_. diff --git a/pyproject.toml b/pyproject.toml index fa2657614..58f3ec772 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ classifiers = [ "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering :: GIS", ] -requires-python = ">=3.8" +requires-python = ">=3.10" dependencies = [ "platformdirs>=2.0.2", "beautifulsoup4>=4.10", @@ -76,7 +76,7 @@ line-length = 88 [tool.ruff] line-length = 88 select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"] -target-version = "py38" +target-version = "py310" ignore = [ "B006", "B008", From 60c275cc640bd909e211c160b4441361f5d54e6e Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 13:00:46 -0400 Subject: [PATCH 3/9] update, cleanup, & organize deps --- .github/workflows/build_docs.yml | 2 +- .github/workflows/unittests.yml | 2 +- ci/{310-minimal.yaml => 310-oldest.yaml} | 19 ++++++---- ci/310.yaml | 20 +++++------ ci/311.yaml | 17 +++++---- ci/312-dev.yaml | 21 ++++++----- ci/312-no-optional.yaml | 8 +++-- ci/312.yaml | 26 ++++++++++---- environment.yml | 44 ++++++++++-------------- pyproject.toml | 38 ++++++++++++-------- 10 files changed, 110 insertions(+), 87 deletions(-) rename ci/{310-minimal.yaml => 310-oldest.yaml} (58%) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 567a18911..fd396b0da 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -20,7 +20,7 @@ strategy: matrix: os: ['ubuntu-latest'] - environment-file: [ci/310.yaml] + environment-file: [ci/312.yaml] experimental: [false] defaults: run: diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml index a8b1bdc38..4e2237f76 100644 --- a/.github/workflows/unittests.yml +++ b/.github/workflows/unittests.yml @@ -24,7 +24,7 @@ jobs: matrix: os: [ubuntu-latest] environment-file: - - ci/310-minimal.yaml + - ci/310-oldest.yaml - ci/310.yaml - ci/311.yaml - ci/312.yaml diff --git a/ci/310-minimal.yaml b/ci/310-oldest.yaml similarity index 58% rename from ci/310-minimal.yaml rename to ci/310-oldest.yaml index 31dee52df..b302c356c 100644 --- a/ci/310-minimal.yaml +++ b/ci/310-oldest.yaml @@ -4,25 +4,30 @@ channels: dependencies: - python=3.10 - beautifulsoup4=4.10 + - geopandas=0.10.0 - jinja2=3.0 + - numpy=1.20 + - packaging=22 - pandas=1.4 + - requests=2.27 - scipy=1.8 + - shapely=2.0.1 - xarray=0.18 # testing - codecov - - matplotlib + - matplotlib>=3.6 - pytest - pytest-cov + - pytest-mpl - pytest-xdist # optional - - geopandas>=0.10.0,<0.13 - - shapely==2.0.1 - - joblib + - geodatasets=2023.3.0 + - joblib>=1.2 - networkx=2.7 - - numba=0.54 - - packaging + - numba=0.55 + - pyarrow>=7.0 + - scikit-learn=1.1 - zstd - - geodatasets - pip - pip: - platformdirs==2.0.2 diff --git a/ci/310.yaml b/ci/310.yaml index 3e0a60ccd..54b4edb41 100644 --- a/ci/310.yaml +++ b/ci/310.yaml @@ -3,30 +3,28 @@ channels: - conda-forge dependencies: - python=3.10 - - platformdirs - beautifulsoup4 + - geopandas - jinja2 + - packaging - pandas + - platformdirs + - requests - scipy + - shapely - xarray # testing - codecov - matplotlib - pytest - pytest-cov + - pytest-mpl - pytest-xdist # optional - - geopandas + - geodatasets - joblib - networkx - numba - - packaging - - zstd - - geodatasets - pyarrow - # for docs build action (this env only) - - nbsphinx - - numpydoc - - sphinx - - sphinxcontrib-bibtex - - sphinx_bootstrap_theme + - scikit-learn + - zstd diff --git a/ci/311.yaml b/ci/311.yaml index 1798e9929..00988bc1d 100644 --- a/ci/311.yaml +++ b/ci/311.yaml @@ -3,25 +3,28 @@ channels: - conda-forge dependencies: - python=3.11 - - platformdirs - beautifulsoup4 + - geopandas - jinja2 + - packaging - pandas + - platformdirs + - requests - scipy + - shapely - xarray # testing - codecov - matplotlib - pytest - pytest-cov + - pytest-mpl - pytest-xdist # optional - - geopandas>=0.12.0 + - geodatasets - joblib - networkx - - packaging - - shapely>=2.0b1 - - xarray - - zstd - - geodatasets + - numba - pyarrow + - scikit-learn + - zstd diff --git a/ci/312-dev.yaml b/ci/312-dev.yaml index 925d44563..3723917b4 100644 --- a/ci/312-dev.yaml +++ b/ci/312-dev.yaml @@ -3,33 +3,36 @@ channels: - conda-forge dependencies: - python=3.12 - - platformdirs - beautifulsoup4 - jinja2 + - platformdirs + - requests # testing - codecov - matplotlib - pytest - pytest-cov + - pytest-mpl - pytest-xdist # optional - - geos - - pyproj + - Cython - fiona + - geodatasets + - geos - joblib - networkx + - numba - packaging - - zstd - - Cython - - geodatasets - pyarrow + - pyproj + - zstd - pip - pip: # dev versions of packages - --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple - - scipy - pandas - - xarray - scikit-learn - - git+https://github.com/shapely/shapely.git@main + - scipy + - xarray - git+https://github.com/geopandas/geopandas.git@main + - git+https://github.com/shapely/shapely.git@main diff --git a/ci/312-no-optional.yaml b/ci/312-no-optional.yaml index becf7bba7..59e0a35cf 100644 --- a/ci/312-no-optional.yaml +++ b/ci/312-no-optional.yaml @@ -3,10 +3,13 @@ channels: - conda-forge dependencies: - python=3.12 - - platformdirs - beautifulsoup4 + - fiona + - geopandas-base>=0.12.0 # base to avoid pulling sklearn - jinja2 - pandas + - platformdirs + - requests - scipy - xarray # testing @@ -14,8 +17,7 @@ dependencies: - matplotlib - pytest - pytest-cov + - pytest-mpl - pytest-xdist # optional used in ci - - geopandas-base>=0.12.0 # base to avoid pulling sklearn - - fiona - geodatasets diff --git a/ci/312.yaml b/ci/312.yaml index cefb868b0..7f8a67070 100644 --- a/ci/312.yaml +++ b/ci/312.yaml @@ -3,25 +3,37 @@ channels: - conda-forge dependencies: - python=3.12 - - platformdirs - beautifulsoup4 + - geopandas - jinja2 + - packaging - pandas + - platformdirs + - requests - scipy + - shapely - xarray # testing - codecov - matplotlib - pytest - pytest-cov + - pytest-mpl - pytest-xdist # optional - - geopandas>=0.12.0 + - geodatasets - joblib - networkx - - packaging - - shapely>=2.0b1 - - xarray - - zstd - - geodatasets + - numba - pyarrow + - scikit-learn + - zstd + # for docs build action (this env only) + - mkdocs-jupyter + - myst-parser + - nbsphinx + - numpydoc + - pandoc + - sphinx + - sphinxcontrib-bibtex + - sphinx_bootstrap_theme diff --git a/environment.yml b/environment.yml index d917c91fc..70a37d268 100644 --- a/environment.yml +++ b/environment.yml @@ -2,35 +2,27 @@ name: libpysal channels: - conda-forge dependencies: + # core env deps + - python - jupyterlab + # core libpysal deps - beautifulsoup4 + - geopandas + - jinja2 + - packaging - pandas + - platformdirs - requests - - jinja2 - - numpydoc - - nbsphinx - - pandoc - - sphinx - - sphinxcontrib-bibtex - - sphinx_bootstrap_theme - - bokeh>=0.11.1 - - folium>=0.2.1 - - geojson>=1.3.2 - - geopandas>=0.2 - - matplotlib>=1.5.1 - - mplleaflet>=0.0.5 - - numba - - numexpr - - networkx - - scikit-learn>=0.17.1 - - seaborn>=0.7.0 - - sqlalchemy - - statsmodels>=0.6.1 + - scipy + - shapely - xarray - - codecov + # optional libpysal deps + - geodatasets - joblib - - packaging - - pytest - - pytest-cov - - pytest-xdist - - mapclassify + - matplotlib + - networkx + - numba + - pyarrow + - scikit-learn + - sqlalchemy + - zstd diff --git a/pyproject.toml b/pyproject.toml index 58f3ec772..66d08a1e2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,15 +25,16 @@ classifiers = [ ] requires-python = ">=3.10" dependencies = [ - "platformdirs>=2.0.2", "beautifulsoup4>=4.10", - "geopandas>=0.9", - "shapely>=2", + "geopandas>=0.10.0", "numpy>=1.20", + "packaging>=22" "pandas>=1.4", - "requests", + "platformdirs>=2.0.2", + "requests>=2.27", "scipy>=1.8", - "packaging" + "shapely>=2.0.1", + "xarray>=0.18", ] [project.urls] @@ -41,30 +42,37 @@ Home = "https://github.com/pysal/libpysal/" Repository = "https://github.com/pysal/libpysal" [project.optional-dependencies] -dev = ["pre-commit"] +plus = [ + "joblib>=1.2", + "networkx>=2.7", + "numba>=0.55", + "pyarrow>=7.0" + "scikit-learn>=1.1" + "zstd" +] +dev = [ + "black", + "pre-commit", + "watermark", +] docs = [ + "mkdocs-jupyter", + "myst-parser" "nbsphinx", "numpydoc", "pandoc", "sphinx", "sphinxcontrib-bibtex", "sphinx_bootstrap_theme", - "mkdocs-jupyter", - "myst-parser" ] tests = [ - "geopandas", "codecov", - "coverage", + "geodatasets>=2023.3.0", + "matplotlib>=3.6", "pytest", "pytest-mpl", "pytest-cov", - "watermark", - "pyarrow", "pytest-xdist", - "matplotlib", - "geodatasets", - "black" ] [tool.setuptools.packages.find] From 907f015900c597040fca7ad46cc1196bae756983 Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 13:08:23 -0400 Subject: [PATCH 4/9] fix pyproject.toml syntax --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 66d08a1e2..6204453ad 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ dependencies = [ "beautifulsoup4>=4.10", "geopandas>=0.10.0", "numpy>=1.20", - "packaging>=22" + "packaging>=22", "pandas>=1.4", "platformdirs>=2.0.2", "requests>=2.27", From 0e669103cb20ce3a9bac26db0f93e067523ea3a5 Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 13:17:08 -0400 Subject: [PATCH 5/9] adjust min pins [1] --- ci/310-oldest.yaml | 4 ++-- pyproject.toml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ci/310-oldest.yaml b/ci/310-oldest.yaml index b302c356c..95637c83f 100644 --- a/ci/310-oldest.yaml +++ b/ci/310-oldest.yaml @@ -6,13 +6,13 @@ dependencies: - beautifulsoup4=4.10 - geopandas=0.10.0 - jinja2=3.0 - - numpy=1.20 + - numpy=1.23 - packaging=22 - pandas=1.4 - requests=2.27 - scipy=1.8 - shapely=2.0.1 - - xarray=0.18 + - xarray=2022.3 # testing - codecov - matplotlib>=3.6 diff --git a/pyproject.toml b/pyproject.toml index 6204453ad..27cb9360e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,14 +27,14 @@ requires-python = ">=3.10" dependencies = [ "beautifulsoup4>=4.10", "geopandas>=0.10.0", - "numpy>=1.20", + "numpy>=1.23", "packaging>=22", "pandas>=1.4", "platformdirs>=2.0.2", "requests>=2.27", "scipy>=1.8", "shapely>=2.0.1", - "xarray>=0.18", + "xarray>=2022.3", ] [project.urls] From 43848eba299e0d372771d457b132dc0093dac48f Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 13:22:39 -0400 Subject: [PATCH 6/9] adjust min pins [2] --- ci/310-oldest.yaml | 2 +- pyproject.toml | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/ci/310-oldest.yaml b/ci/310-oldest.yaml index 95637c83f..5ffe7f1a6 100644 --- a/ci/310-oldest.yaml +++ b/ci/310-oldest.yaml @@ -6,7 +6,7 @@ dependencies: - beautifulsoup4=4.10 - geopandas=0.10.0 - jinja2=3.0 - - numpy=1.23 + - numpy=1.22 - packaging=22 - pandas=1.4 - requests=2.27 diff --git a/pyproject.toml b/pyproject.toml index 27cb9360e..bc98a3667 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ requires-python = ">=3.10" dependencies = [ "beautifulsoup4>=4.10", "geopandas>=0.10.0", - "numpy>=1.23", + "numpy>=1.22", "packaging>=22", "pandas>=1.4", "platformdirs>=2.0.2", @@ -46,9 +46,9 @@ plus = [ "joblib>=1.2", "networkx>=2.7", "numba>=0.55", - "pyarrow>=7.0" - "scikit-learn>=1.1" - "zstd" + "pyarrow>=7.0", + "scikit-learn>=1.1", + "zstd", ] dev = [ "black", @@ -57,7 +57,7 @@ dev = [ ] docs = [ "mkdocs-jupyter", - "myst-parser" + "myst-parser", "nbsphinx", "numpydoc", "pandoc", From a45e153dd876a27a92010a5a3ec8e31e4aa4c744 Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 14:38:42 -0400 Subject: [PATCH 7/9] no numba in 3.12 CI (for now) --- ci/312-dev.yaml | 2 +- ci/312.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/312-dev.yaml b/ci/312-dev.yaml index 3723917b4..7a40eb72f 100644 --- a/ci/312-dev.yaml +++ b/ci/312-dev.yaml @@ -21,7 +21,7 @@ dependencies: - geos - joblib - networkx - - numba + # - numba # follow up when numba is ready for 3.12 - packaging - pyarrow - pyproj diff --git a/ci/312.yaml b/ci/312.yaml index 7f8a67070..72c0bdd97 100644 --- a/ci/312.yaml +++ b/ci/312.yaml @@ -24,7 +24,7 @@ dependencies: - geodatasets - joblib - networkx - - numba + # - numba # follow up when numba is ready for 3.12 - pyarrow - scikit-learn - zstd From 3e24435fd6df6232ef316648b811d483dbbdff1a Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 15:11:14 -0400 Subject: [PATCH 8/9] need proper version in in GHA --- .github/workflows/build_docs.yml | 8 +++++--- .github/workflows/release_and_publish.yml | 3 +++ .github/workflows/unittests.yml | 10 +++++++--- 3 files changed, 15 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index fd396b0da..4ee7ba971 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -27,8 +27,10 @@ shell: bash -l {0} steps: - - name: Checkout repo - uses: actions/checkout@v4 + - name: Checkout repo + uses: actions/checkout@v4 + with: + fetch-depth: 0 # Fetch all history for all branches and tags. - name: Setup micromamba uses: mamba-org/setup-micromamba@v1 @@ -54,7 +56,7 @@ # The above command will fail if no changes were present, # so we ignore the return code. - - name: push to gh-pages + - name: Push to gh-pages uses: ad-m/github-push-action@master with: branch: gh-pages diff --git a/.github/workflows/release_and_publish.yml b/.github/workflows/release_and_publish.yml index 99fc9b434..dade61228 100644 --- a/.github/workflows/release_and_publish.yml +++ b/.github/workflows/release_and_publish.yml @@ -25,9 +25,12 @@ build: name: Create release & publish to PyPI runs-on: ubuntu-latest + steps: - name: Checkout repo uses: actions/checkout@v4 + with: + fetch-depth: 0 # Fetch all history for all branches and tags. - name: Set up python uses: actions/setup-python@v4 diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml index 4e2237f76..f5c1f92c9 100644 --- a/.github/workflows/unittests.yml +++ b/.github/workflows/unittests.yml @@ -40,9 +40,12 @@ jobs: shell: bash -l {0} steps: - - uses: actions/checkout@v4 + - name: Checkout repo + uses: actions/checkout@v4 + with: + fetch-depth: 0 # Fetch all history for all branches and tags. - - name: setup micromamba + - name: Setup micromamba uses: mamba-org/setup-micromamba@v1 with: environment-file: ${{ matrix.environment-file }} @@ -55,7 +58,8 @@ jobs: run: | pytest -v --color yes --cov libpysal --cov-append --cov-report term-missing --cov-report xml . - - uses: codecov/codecov-action@v3 + - name: Codecov + uses: codecov/codecov-action@v3 - name: Generate and publish the report if: | From 3f3b427b2fe78ac5c2d20ce1484b405f52596976 Mon Sep 17 00:00:00 2001 From: James Gaboardi Date: Sat, 21 Oct 2023 15:15:50 -0400 Subject: [PATCH 9/9] fix build_docs indent --- .github/workflows/build_docs.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 4ee7ba971..16d92b33f 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -27,11 +27,11 @@ shell: bash -l {0} steps: - - name: Checkout repo - uses: actions/checkout@v4 - with: - fetch-depth: 0 # Fetch all history for all branches and tags. - + - name: Checkout repo + uses: actions/checkout@v4 + with: + fetch-depth: 0 # Fetch all history for all branches and tags. + - name: Setup micromamba uses: mamba-org/setup-micromamba@v1 with: