From 83cec6277e47d5f0b7a3b64aa155463623e4955a Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Wed, 21 Jan 2026 18:20:04 -0700
Subject: [PATCH 1/6] update deployment workflow

- fix #153
- replaced MDAnalysis/pypi-deployment action with explicit steps
  (see also MDAnalysis/pypi-deployment#11 for details on issues)
- include full tests of installed packages
---
 .github/workflows/deploy.yaml | 203 +++++++++++++++++++++++++++++-----
 1 file changed, 174 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index e53330e..b91f6d8 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -8,48 +8,193 @@ on:
     types:
       - published
 
+concurrency:
+  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+  
+
 jobs:
-  testpypi_push:
-    environment:
-      name: deploy
-      url: https://test.pypi.org/p/GridDataFormats
-    permissions:
-      id-token: write
-    if: |
-      github.repository == 'MDAnalysis/GridDataFormats' &&
-      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
-    name: Build, upload and test pure Python wheels to TestPypi
+  build:
+    name: Build package
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package (binary wheel and source distribution package)
+        run: |
+          python -m build
+
+      - name: Check package
+        run: |
+          twine check dist/*
+
+      - name: Upload dist files
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist-files
+          path: dist/
+          retention-days: 1
+
+  test-install:
+    name: Test package installation
     runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Download dist files
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-files
+          path: dist/
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install dist/*.whl
+
+      - name: Run tests
+        run: |
+          python -c "import gridData; print(f'Package {gridData.__version__} imported successfully')"
 
+  test-pytest:
+    name: Run tests
+    runs-on: ubuntu-latest
+    needs: build
     steps:
-      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
 
-      - name: testpypi_deploy
-        uses: MDAnalysis/pypi-deployment@main
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+      - name: Download dist files
+        uses: actions/download-artifact@v4
         with:
-          test_submission: true
-          package_name: GridDataFormats
-          module_name: 'gridData'
+          name: dist-files
+          path: dist/
+
+      - name: Install package with test dependencies and tests
+        run: |
+          python -m pip install --upgrade pip
+          WHEEL_FILE=$(ls dist/*.whl)
+          pip install "$WHEEL_FILE"[test]
+
+      - name: Run tests
+        run: |
+          pytest --verbose --pyargs gridData
 
-  pypi_push:
+  deploy-testpypi:
+    name: Deploy to TestPyPI
+    runs-on: ubuntu-latest
+    needs: [build, test-install, test-pytest]
+    if: |
+      github.repository == 'MDAnalysis/GridDataFormats' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
     environment:
-      name: deploy
-      url: https://pypi.org/p/GridDataFormats
+      name: testpypi
+      url: https://test.pypi.org/p/GridDataFormats
     permissions:
-      id-token: write
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download dist files
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-files
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@v1.12.4
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  deploy-pypi:
+    name: Deploy to PyPI
+    runs-on: ubuntu-latest
+    needs: [build, test-install, test-pytest]
     if: |
       github.repository == 'MDAnalysis/GridDataFormats' &&
       (github.event_name == 'release' && github.event.action == 'published')
-    name: Build, upload and test pure Python wheels to PyPi
-    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/GridDataFormats
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download dist files
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-files
+          path: dist/
 
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.12.4
+
+  test-deployed-testpypi:
+    name: Test deployed package (TestPyPI)
+    runs-on: ubuntu-latest
+    needs: deploy-testpypi
+    if: |
+      github.repository == 'MDAnalysis/GridDataFormats' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
     steps:
-      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
 
-      - name: pypi_deploy
-        uses: MDAnalysis/pypi-deployment@main
-        if: github.event_name == 'release' && github.event.action == 'published'
+      - name: Install from TestPyPI
+        run: |
+          python -m pip install --upgrade pip
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ GridDataFormats[test]
+
+      - name: Test import
+        run: |
+          python -c "import gridData; print(f'Package {gridData.__version__} imported successfully from TestPyPi')"
+
+      - name: Run basic tests
+        run: |
+          pytest --verbose --pyargs gridData
+
+  test-deployed-pypi:
+    name: Test deployed package (PyPI)
+    runs-on: ubuntu-latest
+    needs: deploy-pypi
+    if: |
+      github.repository == 'MDAnalysis/GridDataFormats' &&
+      (github.event_name == 'release' && github.event.action == 'published')
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          package_name: GridDataFormats
-          module_name: 'gridData'
+          python-version: "3.x"
+
+      - name: Install from PyPI
+        run: |
+          python -m pip install --upgrade pip
+          pip install GridDataFormats[test]
+
+      - name: Test import
+        run: |
+          python -c "import gridData; print(f'Package {gridData.__version__} imported successfully from PyPi')"
+
+      - name: Run basic tests
+        run: |
+          pytest --verbose --pyargs gridData

From 0e4be241a0dcccd3976a6f3d4bebf4b89c721f8d Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Wed, 21 Jan 2026 18:40:03 -0700
Subject: [PATCH 2/6] removed outdated license identifier

- fix #155
- add license files explicitly
- use LGPL 3.0+ identifier
---
 MANIFEST.in    | 2 +-
 pyproject.toml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index f17a4a7..1ddb7ab 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
 include README.rst INSTALL CHANGELOG COPYING COPYING.LESSER AUTHORS
-include setup.py
+
 
diff --git a/pyproject.toml b/pyproject.toml
index 60dbce0..7e7d044 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,8 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "GridDataFormats"
 description = "Reading and writing of data on regular grids in Python"
-license = {file = "COPYING.LESSER" }
+license = "LGPL-3.0-or-later"
+license-files = ["COPYING", "COPYING.LESSER", "AUTHORS"]
 authors = [
     {name = "Oliver Beckstein", email = "orbeckst@gmail.com"},
 ]
@@ -19,7 +20,6 @@ classifiers = [
     "Development Status :: 6 - Mature",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
     "Operating System :: POSIX",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: Microsoft :: Windows",

From ad6c44738f4d817df0f8714eb515993fa8885ca0 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Wed, 21 Jan 2026 18:55:54 -0700
Subject: [PATCH 3/6] fix missing tests in distribution

- fix #156
- explicitly list tests and tests.datafiles to be included
---
 pyproject.toml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7e7d044..f1b9c7b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,12 +60,11 @@ documentation = "https://www.mdanalysis.org/GridDataFormats/"
 
 [tool.setuptools]
 zip-safe = true
-include-package-data = true
 
 [tool.setuptools.packages.find]
 namespaces = false
-include=["gridData"]
-exclude=["devtools", "doc", "ci", "examples"]
+include = ["gridData", "gridData.tests", "gridData.tests.datafiles"]
+exclude = ["devtools", "doc", "ci", "examples"]
 
 [tool.setuptools.package-data]
 gridData = [

From e94676d68942abe148f42ee14a0a5adf6eb58668 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Thu, 22 Jan 2026 09:01:16 -0700
Subject: [PATCH 4/6] include mrc test files in distribution

MRC files were left out from the distribution in PR #149.
This commit adds them via explicit inclusion pattern in the pyproject.toml file
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index f1b9c7b..4f9bcf0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,6 +71,7 @@ gridData = [
     "tests/datafiles/*.dx",
     "tests/datafiles/*.dx.gz",
     "tests/datafiles/*.ccp4",
+    "tests/datafiles/*.mrc",
     "tests/datafiles/*.plt",
     "tests/datafiles/*.bz2",
 ]

From d38bbd860ffa35c072e4d08e5f69f1bfe811a209 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Thu, 22 Jan 2026 09:28:50 -0700
Subject: [PATCH 5/6] updated and finalized CHANGELOG

---
 CHANGELOG | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index d193c8f..f3b2700 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -13,7 +13,7 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 -------------------------------------------------------------------------------
-01/16/2026 IAlibay, ollyfutur, conradolandia, orbeckst, PlethoraChutney, 
+01/22/2026 IAlibay, ollyfutur, conradolandia, orbeckst, PlethoraChutney,
            Pradyumn-cloud
 
   * 1.1.0
@@ -24,10 +24,11 @@ The rules for this file:
     (issue #143)
   * Python 3.13 and 3.14 are now supported (PR #140)
   * Support for Python 3.9 and 3.10 is now dropped as per SPEC0 (PR #140)
+  * all tests and data files are now included in the distribution (#156)
 
   Enhancements
 
-  * `Grid` now accepts binary operations with any operand that can be 
+  * `Grid` now accepts binary operations with any operand that can be
     broadcasted to the grid's shape according to `numpy` broadcasting rules
     (PR #142)
   * `Grid` now allows forcing MRC/CCP4 maps to be read as volumes even when
@@ -38,6 +39,7 @@ The rules for this file:
 
   * Attempting binary operations on grids with different edges now raises an
     exception (PR #142)
+  * updated metadata license identifier (#155)
 
 
 10/21/2023 IAlibay, orbeckst, lilyminium

From 80afbd21a26bb637629e623d8c663a5d21b67185 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Thu, 22 Jan 2026 12:00:30 -0700
Subject: [PATCH 6/6] update deployment workflow

- run on Python 3.14
- test deployed packages on ubuntu and macos latest
  fail-fast: false to allow others to run so that we can see tests on different
  OSs succeeding/failing
- concurrency: allow push/tag and release runs to both complete

Co-authored-by: Irfan Alibay <ialibay@mdanalysis.org>
---
 .github/workflows/deploy.yaml | 61 ++++++++++++++---------------------
 1 file changed, 24 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index b91f6d8..e1cca34 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -10,7 +10,7 @@ on:
 
 concurrency:
   group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 defaults:
   run:
@@ -28,7 +28,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
+          python-version: "3.14"
 
       - name: Install build dependencies
         run: |
@@ -50,31 +50,6 @@ jobs:
           path: dist/
           retention-days: 1
 
-  test-install:
-    name: Test package installation
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.x"
-
-      - name: Download dist files
-        uses: actions/download-artifact@v4
-        with:
-          name: dist-files
-          path: dist/
-
-      - name: Install package
-        run: |
-          python -m pip install --upgrade pip
-          pip install dist/*.whl
-
-      - name: Run tests
-        run: |
-          python -c "import gridData; print(f'Package {gridData.__version__} imported successfully')"
-
   test-pytest:
     name: Run tests
     runs-on: ubuntu-latest
@@ -83,7 +58,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
+          python-version: "3.14"
 
       - name: Download dist files
         uses: actions/download-artifact@v4
@@ -97,14 +72,18 @@ jobs:
           WHEEL_FILE=$(ls dist/*.whl)
           pip install "$WHEEL_FILE"[test]
 
-      - name: Run tests
+      - name: Test import
+        run: |
+          python -c "import gridData; print(f'Package {gridData.__version__} imported successfully')"
+          
+      - name: Run basic tests
         run: |
           pytest --verbose --pyargs gridData
 
   deploy-testpypi:
     name: Deploy to TestPyPI
     runs-on: ubuntu-latest
-    needs: [build, test-install, test-pytest]
+    needs: [build, test-pytest]
     if: |
       github.repository == 'MDAnalysis/GridDataFormats' &&
       (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
@@ -121,14 +100,14 @@ jobs:
           path: dist/
 
       - name: Publish to TestPyPI
-        uses: pypa/gh-action-pypi-publish@v1.12.4
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           repository-url: https://test.pypi.org/legacy/
 
   deploy-pypi:
     name: Deploy to PyPI
     runs-on: ubuntu-latest
-    needs: [build, test-install, test-pytest]
+    needs: [build, test-pytest]
     if: |
       github.repository == 'MDAnalysis/GridDataFormats' &&
       (github.event_name == 'release' && github.event.action == 'published')
@@ -145,11 +124,15 @@ jobs:
           path: dist/
 
       - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.12.4
+        uses: pypa/gh-action-pypi-publish@v1.13.0
 
   test-deployed-testpypi:
     name: Test deployed package (TestPyPI)
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
     needs: deploy-testpypi
     if: |
       github.repository == 'MDAnalysis/GridDataFormats' &&
@@ -158,7 +141,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
+          python-version: "3.14"
 
       - name: Install from TestPyPI
         run: |
@@ -175,7 +158,11 @@ jobs:
 
   test-deployed-pypi:
     name: Test deployed package (PyPI)
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
     needs: deploy-pypi
     if: |
       github.repository == 'MDAnalysis/GridDataFormats' &&
@@ -184,7 +171,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
+          python-version: "3.14"
 
       - name: Install from PyPI
         run: |