Merge branch 'main' into faster_import_time

.github/workflows/docs.yml

@@ -42,7 +42,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # Need to fetch more than the last commit so that setuptools-scm can
           # create the correct version string. If the number of commits since
@@ -58,9 +58,9 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.x"
 
       - name: Collect requirements
         run: |
@@ -86,7 +86,7 @@ jobs:
           echo "::set-output name=dir::$(pip cache dir)"
 
       - name: Setup caching for pip packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           key: ${{ runner.os }}-pip-${{ hashFiles('requirements-full.txt') }}
@@ -113,7 +113,7 @@ jobs:
 
       # Store the docs as a build artifact so we can deploy it later
       - name: Upload HTML documentation as an artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: docs-${{ github.sha }}
           path: doc/_build/html
@@ -127,11 +127,11 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       # Fetch the built docs from the "build" job
       - name: Download HTML documentation artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: docs-${{ github.sha }}
           path: doc/_build/html

.github/workflows/pypi.yml

@@ -29,7 +29,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # Need to fetch more than the last commit so that setuptools_scm can
           # create the correct version string. If the number of commits since
@@ -45,9 +45,9 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.x"
 
       - name: Install requirements
         run: |
@@ -79,7 +79,7 @@ jobs:
       - name: Upload archives as artifacts
         # Only if not a pull request
         if: success() && github.event_name != 'pull_request'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: pypi-${{ github.sha }}
           path: dist
@@ -94,15 +94,15 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # The GitHub token is preserved by default but this job doesn't need
           # to be able to push to GitHub.
           persist-credentials: false
 
       # Fetch the built archives from the "build" job
       - name: Download built archives artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: pypi-${{ github.sha }}
           path: dist

.github/workflows/style.yml

@@ -20,12 +20,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.10"
 
@@ -42,12 +42,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.10"
 

.github/workflows/test.yml

@@ -20,15 +20,14 @@ on:
   schedule:
     # Run every Monday at 12:00 UTC
     # * is a special character in YAML so you have to quote this string
-    - cron:  '00 12 * * 1'
+    - cron: "00 12 * * 1"
 
 # Use bash by default in all jobs
 defaults:
   run:
     shell: bash
 
 jobs:
-
   #############################################################################
   # Run tests and upload to codecov
   test:
@@ -45,7 +44,7 @@ jobs:
           - windows
         python:
           - "3.7"
-          - "3.10"
+          - "3.11"
         dependencies:
           - latest
           - optional
@@ -68,7 +67,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # Need to fetch more than the last commit so that setuptools-scm can
           # create the correct version string. If the number of commits since
@@ -84,7 +83,7 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
 
@@ -119,7 +118,7 @@ jobs:
           echo "::set-output name=dir::$(pip cache dir)"
 
       - name: Setup caching for pip packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           key: ${{ runner.os }}-pip-${{ hashFiles('requirements-full.txt') }}
@@ -148,9 +147,9 @@ jobs:
         run: coverage xml
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
-          file: ./coverage.xml
+          files: ./coverage.xml
           env_vars: OS,PYTHON,DEPENDENCIES
           # Don't mark the job as failed if the upload fails for some reason.
           # It does sometimes but shouldn't be the reason for running

AUTHORS.md

@@ -13,6 +13,7 @@ order by last name) and are considered "The Pooch Developers":
 * [Dominic Kempf](https://github.com/dokempf) - Scientific Software Center, Heidelberg University, Germany (ORCID: [0000-0002-6140-2332](https://www.orcid.org/0000-0002-6140-2332))
 * [Kacper Kowalik](https://github.com/Xarthisius) - National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, USA (ORCID: [0000-0003-1709-3744](https://www.orcid.org/0000-0003-1709-3744))
 * [John Leeman](https://github.com/jrleeman)
+* [Björn Ludwig](https://github.com/BjoernLudwigPTB) - Physikalisch-Technische Bundesanstalt, Germany (ORCID: [0000-0002-5910-9137](https://www.orcid.org/0000-0002-5910-9137))
 * [Daniel McCloy](https://github.com/drammock) - University of Washington, USA (ORCID: [0000-0002-7572-3241](https://orcid.org/0000-0002-7572-3241))
 * [Rémi Rampin](https://github.com/remram44) - New York University, USA (ORCID: [0000-0002-0524-2282](https://www.orcid.org/0000-0002-0524-2282))
 * [Clément Robert](https://github.com/neutrinoceros) - Institut de Planétologie et d'Astrophysique de Grenoble, France (ORCID: [0000-0001-8629-7068](https://orcid.org/0000-0001-8629-7068))

CITATION.rst

@@ -14,5 +14,20 @@ If you used Pooch in your research, please consider citing our paper:
 This is an open-access publication. The paper and the associated software
 review can be freely accessed at: https://doi.org/10.21105/joss.01943
 
-If you need a Bibtex entry for the paper, grab it here:
-https://www.doi2bib.org/bib/10.21105/joss.01943
+Here is a Bibtex entry to make things easier if you’re using Latex:
+
+.. code:: bibtex
+
+    @article{uieda2020,
+      title = {{Pooch}: {A} friend to fetch your data files},
+      author = {Leonardo Uieda and Santiago Soler and R{\'{e}}mi Rampin and Hugo van Kemenade and Matthew Turk and Daniel Shapero and Anderson Banihirwe and John Leeman},
+      year = {2020},
+      doi = {10.21105/joss.01943},
+      url = {https://doi.org/10.21105/joss.01943},
+      month = jan,
+      publisher = {The Open Journal},
+      volume = {5},
+      number = {45},
+      pages = {1943},
+      journal = {Journal of Open Source Software}
+    }

README.md

@@ -149,6 +149,7 @@ def fetch_gravity_data():
 * [climlab](https://github.com/climlab/climlab)
 * [napari](https://github.com/napari/napari)
 * [mne-python](https://github.com/mne-tools/mne-python)
+* [GemGIS](https://github.com/cgre-aachen/gemgis)
 
 *If you're using Pooch, send us a pull request adding your project to the list.*
 

doc/changes.rst

@@ -3,6 +3,64 @@
 Changelog
 =========
 
+Version 1.7.0
+-------------
+
+*Released on: 2023/02/27*
+
+doi:`10.5281/zenodo.7678844 <https://doi.org/10.5281/zenodo.7678844>`__
+
+Bug fixes:
+
+* Make archive extraction always take members into account (`#316 <https://github.com/fatiando/pooch/pull/316>`__)
+* Figshare downloaders fetch the correct version, instead of always the latest one. (`#343 <https://github.com/fatiando/pooch/pull/343>`__)
+
+New features:
+
+* Allow spaces in filenames in registry files (`#315 <https://github.com/fatiando/pooch/pull/315>`__)
+* Refactor ``Pooch.is_available`` to use downloaders (`#322 <https://github.com/fatiando/pooch/pull/322>`__)
+* Add support for downloading files from Dataverse DOIs (`#318 <https://github.com/fatiando/pooch/pull/318>`__)
+* Add a new ``Pooch.load_registry_from_doi`` method that populates the Pooch registry using DOI-based data repositories (`#325 <https://github.com/fatiando/pooch/pull/325>`__)
+* Support urls for Zenodo repositories created through the GitHub integration service, which include slashes in the filename of the main zip files (`#340 <https://github.com/fatiando/pooch/pull/340>`__)
+* Automatically add a trailing slash to ``base_url`` on ``pooch.create`` (`#344 <https://github.com/fatiando/pooch/pull/344>`__)
+
+Maintenance:
+
+* Drop support for Python 3.6 (`#299 <https://github.com/fatiando/pooch/pull/299>`__)
+* Port from deprecated ``appdirs`` to ``platformdirs`` (`#339 <https://github.com/fatiando/pooch/pull/339>`__)
+* Update version of Codecov's Action to v3 (`#345 <https://github.com/fatiando/pooch/pull/345>`__)
+
+Documentation:
+
+* Update sphinx, theme, and sphinx-panels (`#300 <https://github.com/fatiando/pooch/pull/300>`__)
+* Add CITATION.cff for the JOSS article (`#308 <https://github.com/fatiando/pooch/pull/308>`__)
+* Use Markdown for the README (`#311 <https://github.com/fatiando/pooch/pull/311>`__)
+* Improve docstring of `known_hash` in `retrieve` function (`#333 <https://github.com/fatiando/pooch/pull/333>`__)
+* Replace link to Pooch's citation with a BibTeX code snippet (`#335 <https://github.com/fatiando/pooch/pull/335>`__)
+
+Projects that started using Pooch:
+
+* Open AR-Sandbox (`#305 <https://github.com/fatiando/pooch/pull/305>`__)
+* ``climlab`` (`#312 <https://github.com/fatiando/pooch/pull/312>`__)
+* SciPy (`#320 <https://github.com/fatiando/pooch/pull/320>`__)
+* ``napari`` (`#321 <https://github.com/fatiando/pooch/pull/321>`__)
+* ``mne-python`` (`#323 <https://github.com/fatiando/pooch/pull/323>`__)
+
+This release contains contributions from:
+
+* Alex Fikl
+* Anirudh Dagar
+* Björn Ludwig
+* Brian Rose
+* Dominic Kempf
+* Florian Wellmann
+* Gabriel Fu
+* Kyle I S Harrington
+* Leonardo Uieda
+* myd7349
+* Rowan Cockett
+* Santiago Soler
+
 Version 1.6.0
 -------------
 

doc/install.rst

@@ -53,7 +53,7 @@ manually.
 
 Required:
 
-* `appdirs <https://github.com/ActiveState/appdirs>`__
+* `platformdirs <https://github.com/platformdirs/platformdirs>`__
 * `packaging <https://github.com/pypa/packaging>`__
 * `requests <https://docs.python-requests.org/>`__
 

doc/protocols.rst

@@ -103,3 +103,24 @@ figshare dataset:
     ``doi:10.6084/m9.figshare.c.4362224.v1``. Attempting to download files
     from a figshare collection will raise an error.
     See `issue #274 <https://github.com/fatiando/pooch/issues/274>`__ details.
+
+Since this type of repositories store information about the files contained in
+them, we can avoid having to manually type the registry with the file names and
+their hashes.
+Instead, we can use the :meth:`pooch.Pooch.load_registry_from_doi` to
+automatically populate the registry:
+
+.. code-block:: python
+
+    POOCH = pooch.create(
+        path=pooch.os_cache("plumbus"),
+        # Use the figshare DOI
+        base_url="doi:10.6084/m9.figshare.14763051.v1/",
+        registry=None,
+    )
+
+    # Automatically populate the registry
+    POOCH.load_registry_from_doi()
+
+    # Fetch one of the files in the repository
+    fname = POOCH.fetch("tiny-data.txt")

doc/versions.rst

@@ -7,6 +7,7 @@ Use the links below to access documentation for specific versions
 * `Latest release <https://www.fatiando.org/pooch/latest>`__
 * `Development <https://www.fatiando.org/pooch/dev>`__
   (reflects the current development branch on GitHub)
+* `v1.7.0 <https://www.fatiando.org/pooch/v1.7.0>`__
 * `v1.6.0 <https://www.fatiando.org/pooch/v1.6.0>`__
 * `v1.5.2 <https://www.fatiando.org/pooch/v1.5.2>`__
 * `v1.5.1 <https://www.fatiando.org/pooch/v1.5.1>`__

environment.yml

@@ -3,12 +3,12 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    - python==3.10
+    - python==3.11
     - pip
     # Run
     - requests
     - packaging
-    - appdirs
+    - platformdirs
     # Build
     - build
     # Test