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revisit _points_as_gdf() #720

Merged
merged 4 commits into from
May 8, 2023
Merged

revisit _points_as_gdf() #720

merged 4 commits into from
May 8, 2023

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jGaboardi
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Follow up from #718 (review).

Is this something along the lines you were thinking, @martinfleis?

@jGaboardi jGaboardi requested a review from martinfleis May 7, 2023 21:54
@jGaboardi jGaboardi self-assigned this May 7, 2023
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Codecov Report

Merging #720 (d0134f4) into main (6ba30c0) will decrease coverage by 0.0%.
The diff coverage is 100.0%.

Impacted file tree graph

@@           Coverage Diff           @@
##            main    #720     +/-   ##
=======================================
- Coverage   97.6%   97.6%   -0.0%     
=======================================
  Files          3       3             
  Lines       1177    1176      -1     
  Branches     300     299      -1     
=======================================
- Hits        1149    1148      -1     
  Misses         7       7             
  Partials      21      21
Impacted Files Coverage Δ
spaghetti/util.py 98.3% <100.0%> (-<0.1%) ⬇️

martinfleis
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@jGaboardi jGaboardi requested a review from martinfleis May 8, 2023 18:00
martinfleis
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I think this is in the end the best solution :).

@jGaboardi jGaboardi merged commit 7dfb5e3 into pysal:main May 8, 2023
@jGaboardi jGaboardi deleted the revisit_gpd_compat branch May 8, 2023 18:05
This was referenced May 8, 2023
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@jGaboardi jGaboardi mentioned this pull request May 27, 2023
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jGaboardi added a commit that referenced this pull request Dec 11, 2023
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jGaboardi:deprecate_pysal_geoms --> pysal:deprecate_pysal_geoms (#754)
3353b74 
* 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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