remove pygeos from environments #696
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Dec 11, 2023
* depwarning for libpysal geometries * more descriptive FutureWarning * Update spaghetti/network.py Co-authored-by: Martin Fleischmann <martin@martinfleischmann.net> * ignore versioneer files in codecov * reduce builds for codecov report * add manual triggers for workflows * access version from pacakge * better solution for version fetch * syntax correction * don't run gitcount in r&p action * remove gitcount notebook * try new automated release notes * updated release notes automation * attempt 3.10 in CI * fix file name * test base and dev on 3.10 * update codecov * slim down testing matrix * slim down testing matrix [2] * slim down testing matrix [3] * streamline matrix logic * try pytest-xdist for multicore tests * update CI environs * update variable syntax * automate core count for tests * set to 8 cores * back to 4 cores * set back to auto cores * unitform syntax - remove = * try env var for pip install * break up line length * trim down line lengths * branch env var * remove branch env var * env vs. environment-file * try env-file * try > yaml line breaks * too much trouble to split pytest command * reinstate environment-file * remove PIP variable * update supported Python versions * update black vers in pre-commit * supported versions in CONTRIB * contact in contrib * support clause in README & docs * update CI badge (#665) * Bump actions/github-script from 5 to 6 Bumps [actions/github-script](https://github.com/actions/github-script) from 5 to 6. - [Release notes](https://github.com/actions/github-script/releases) - [Commits](actions/github-script@v5...v6) --- updated-dependencies: - dependency-name: actions/github-script dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * timeout squared_distance_point_link test * add pytest-timeout requirement * try timeout flag in pytest command * remove local flag * Update unittests.yml * Update release_and_publish.yml * Bump actions/checkout from 2 to 3 Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v3) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump codecov/codecov-action from 2 to 3 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2 to 3. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md) - [Commits](codecov/codecov-action@v2...v3) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * update/rerun notebooks * Update .pre-commit-config.yaml (#673) * no log for tsp notebook * drop 37 testing * update reqs, codecov, etc. * update docs * Bump actions/setup-python from 3 to 4 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 4. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v3...v4) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Update .pre-commit-config.yaml * move to pytest * run isort * autmate linting and code sorting * some clean ups * some clean ups [2] * some clean ups [3] * trigger CI * update test * rerun notebooks * remove docs/* notebooks * resolves #678 * fix indent * one CI to rule them all * pin installed * no pygeos * flexible channel * Update ci/310-DEV_shapely20b1.yaml Co-authored-by: Martin Fleischmann <martin@martinfleischmann.net> * linting in CI * correct action version * updating CI badge (filename) * Bump actions/setup-python from 3 to 4 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 4. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v3...v4) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 22.6.0 → 22.10.0](psf/black@22.6.0...22.10.0) * try 311 and warning handling * attempt DEV 3.11 testing * drop shapely DEV 3.11 testing * forgot to change Py vers in .yml * more robust error testing * add 3.11 ref & binder env. * try micromamba version checking * proper BASE logic * proper BASE logic [2] * proper BASE logic [3] * proper BASE logic [4] * update env file names to accomodate logic * update step name * binder doesn't support python=3.11 * update sphinx tooling, etc. * correct doc build env name * correct CI badge * esda master -> main * adjust css for doc refs * [pre-commit.ci] pre-commit autoupdate (#689) updates: - [github.com/pycqa/flake8: 5.0.4 → 6.0.0](PyCQA/flake8@5.0.4...6.0.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update CONTRIBUTING.md * [pre-commit.ci] pre-commit autoupdate (#691) updates: - [github.com/pycqa/isort: 5.10.1 → 5.11.1](PyCQA/isort@5.10.1...5.11.1) - [github.com/psf/black: 22.10.0 → 22.12.0](psf/black@22.10.0...22.12.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * try pyproject.toml (#690) * [pre-commit.ci] pre-commit autoupdate (#692) updates: - [github.com/pycqa/isort: 5.11.1 → v5.11.3](PyCQA/isort@5.11.1...v5.11.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#693) * resolves #694 (#695) * resolves #680 (#696) * resolves #680 (#696) * try versioneer action (#697) * try versioneer action * unpin versioneer version in pyproject.toml * add toml path to versioneer action * make deps dynamic in toml * update versioneer.yml * correct syntax in versioneer.yml * try pinning versioneer[toml]==0.28 * implement versioneer suggestions * update pypa/gh-action-pypi-publish branch * Update Versioneer (#698) * [Bot] Update Versioneer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: jGaboardi <jGaboardi@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update versioneer.yml * Update Versioneer (#699) * [Bot] Update Versioneer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: jGaboardi <jGaboardi@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * add formatting exclusions properly in toml (#702) * Update Versioneer (#700) * [Bot] Update Versioneer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: jGaboardi <jGaboardi@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [Bot] Update Versioneer (#703) Co-authored-by: jGaboardi <jGaboardi@users.noreply.github.com> * address #701 [1] * [pre-commit.ci] pre-commit autoupdate (#706) updates: - [github.com/pycqa/isort: 5.11.4 → 5.12.0](PyCQA/isort@5.11.4...5.12.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [Bot] Update Versioneer (#707) Co-authored-by: jGaboardi <jGaboardi@users.noreply.github.com> * update black pin in pre-commit (#708) * Update testing.yml (#710) * [pre-commit.ci] pre-commit autoupdate (#712) updates: - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Bump peter-evans/create-pull-request from 4 to 5 (#713) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * address #717 (#718) * Fix memory leak in `full_distance_matrix()` (#719) * resolves #715 * no strict kwarg for zip in 3.8 * revisit `_points_as_gdf()` (#720) * revisit _points_as_gdf * use shapely.points() * combined positional arg for points * update shapely verion reqs * Overhaul repo infrastructure (#721) * update pre-commit * update infrastructure * ruff [1] * ruffen repo [2] * update infra [2] * update extract_comp() stacklevel * noqa ARG001 for geom_col for now * refactor element_as_gdf internals (#724) * refactor element_as_gdf internal constructors * deprecate geom_col kwarg in elem_as_gdf * update element_as_gdf() stacklevel * [pre-commit.ci] pre-commit autoupdate (#728) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.265 → v0.0.270](astral-sh/ruff-pre-commit@v0.0.265...v0.0.270) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#730) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.270 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.270...v0.0.272) * new repo --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Martin Fleischmann <martin@martinfleischmann.net> * update micromamba in CI (#732) * update micromamba in CI * add @v1 * Doc patch (#733) * import from module not class * fix pointpats intersphinx link * force reinstall package for version fetching in `build_docs.yaml` (#734) * force renistall for buil_docs.yaml * martin comment * [pre-commit.ci] pre-commit autoupdate (#735) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#736) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#737) updates: - [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0) - [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#739) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * resolve #740 (#741) * Bump actions/checkout from 3 to 4 (#744) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump codecov/codecov-action from 3 to 4 (#745) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Revert "Bump codecov/codecov-action from 3 to 4 (#745)" (#746) This reverts commit 51856f8. * proper README in pyproject.toml (#747) * Linting & Formatting - 2023-10-03 (#749) * update pre-commit * reup linting and formatting * Bump actions/github-script from 6 to 7 (#750) Bumps [actions/github-script](https://github.com/actions/github-script) from 6 to 7. - [Release notes](https://github.com/actions/github-script/releases) - [Commits](actions/github-script@v6...v7) --- updated-dependencies: - dependency-name: actions/github-script dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Provide testing support for Python 3.12 – drop support for {3.8, 3.9} (#751) * update precommit * update CI env * update workflows * Python 312 support - drop 38/39 * update test for Python 312 pass (minor rounding) * update CI versions/syntax * proper dev install of shapely * martin suggestion - geos * matplotlib for esda * matplotlib for esda * stable -> latest * bash evaluator * bash evaluator [2] * not no-optional experssion * not no-optional expression [2] * not no-optional expression [3] * remove section from README * Bump actions/setup-python from 4 to 5 (#753) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Utilize `ruff-format` over `black` for formatting (#752) * update pre-commit * adopt ruff-format over black for formatting * remove commented lines * martin suggestion --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Martin Fleischmann <martin@martinfleischmann.net> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: jGaboardi <jGaboardi@users.noreply.github.com>
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This PR resolves #680.