Resuming maintenance - Basic catch up and fix up of the nox sessions

.github/workflows/build_tests.yml

@@ -48,51 +48,51 @@ jobs:
               run: nox -s build_tests_unit -x -- -vv
 
 
-    documentation_tests:
-        name: "Build documentation testing on ${{ matrix.os }}"
-        runs-on: "${{ matrix.os }}"
-
-        strategy:
-            fail-fast: false
-            matrix:
-                os:
-                    - ubuntu-latest
-                    - macos-latest
-
-        steps:
-            - name: "Check out the repo"
-              uses: "actions/checkout@v4"
-
-            - name: "Set up Python"
-              uses: "actions/setup-python@v5"
-              with:
-                  python-version: |
-                    3.10
-                    3.11
-                    3.12
-
-            - name: "Install dependencies"
-              run: |
-                  python -m pip install --upgrade pip
-                  python -m pip install nox poetry
-                  poetry self add poetry-plugin-export
-
-            - name: "Get public IP address of runner"
-              # Need to handle this for Windows, MacOS, and linux
-              # Fetch from ipinfo.io/ip and echo it
-              run: |
-                  if [[ "$RUNNER_OS" == "Windows" ]]; then
-                    echo "Windows runner IP: $(curl -s https://ipinfo.io/ip)"
-                  elif [[ "$RUNNER_OS" == "macOS" ]]; then
-                    echo "macOS runner IP: $(curl -s https://ipinfo.io/ip)"
-                  else
-                    echo "Linux runner IP: $(curl -s https://ipinfo.io/ip)"
-                  fi
-
-            - name: "Run nox"
-              run: |
-                  # Unit tests
-                  python -m nox -s build_tests_scripts --verbose -x -- -vv
+#    documentation_tests:
+#        name: "Build documentation testing on ${{ matrix.os }}"
+#        runs-on: "${{ matrix.os }}"
+#
+#        strategy:
+#            fail-fast: false
+#            matrix:
+#                os:
+#                    - ubuntu-latest
+#                    - macos-latest
+#
+#        steps:
+#            - name: "Check out the repo"
+#              uses: "actions/checkout@v4"
+#
+#            - name: "Set up Python"
+#              uses: "actions/setup-python@v5"
+#              with:
+#                  python-version: |
+#                    3.10
+#                    3.11
+#                    3.12
+#
+#            - name: "Install dependencies"
+#              run: |
+#                  python -m pip install --upgrade pip
+#                  python -m pip install nox poetry
+#                  poetry self add poetry-plugin-export
+#
+#            - name: "Get public IP address of runner"
+#              # Need to handle this for Windows, MacOS, and linux
+#              # Fetch from ipinfo.io/ip and echo it
+#              run: |
+#                  if [[ "$RUNNER_OS" == "Windows" ]]; then
+#                    echo "Windows runner IP: $(curl -s https://ipinfo.io/ip)"
+#                  elif [[ "$RUNNER_OS" == "macOS" ]]; then
+#                    echo "macOS runner IP: $(curl -s https://ipinfo.io/ip)"
+#                  else
+#                    echo "Linux runner IP: $(curl -s https://ipinfo.io/ip)"
+#                  fi
+#
+#            - name: "Run nox"
+#              run: |
+#                  # Unit tests
+#                  python -m nox -s build_tests_scripts --verbose -x -- -vv
 
 
     integration_tests:
@@ -127,6 +127,7 @@ jobs:
               with:
                 python-version: "${{ matrix.python-version }}"
                 conda-remove-defaults: "true"
+                channels: conda-forge
 
             - name: "Install and update pip"
               run: |

.github/workflows/documentation.yml

@@ -16,11 +16,17 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
+        with:
+            python-version: 3.12
       - name: Install dependencies
         run: |
           pip install --upgrade pip
           pip install poetry nox
           poetry self add poetry-plugin-export
+      - name: Install OpenBLAS
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libopenblas-dev liblapack-dev
       - name: Sphinx build
         run: |
           nox -s docs

.github/workflows/source_tests.yml

@@ -68,57 +68,57 @@ jobs:
                   name: covdata
                   path: .coverage.*
 
-    documentation_tests:
-        name: "Documentation testing on ${{ matrix.os }}"
-        runs-on: "${{ matrix.os }}"
-
-        strategy:
-            fail-fast: false
-            matrix:
-                os:
-                    - ubuntu-latest
-                    - macos-latest
-
-        steps:
-            - name: "Check out the repo"
-              uses: "actions/checkout@v4"
-
-            - name: "Set up Python"
-              uses: "actions/setup-python@v5"
-              with:
-                  python-version: |
-                    3.10
-                    3.11
-                    3.12
-
-            - name: "Install dependencies"
-              run: |
-                  python -m pip install --upgrade pip
-                  python -m pip install nox poetry
-                  poetry self add poetry-plugin-export
-
-            - name: "Get public IP address of runner"
-              # Need to handle this for Windows, MacOS, and linux
-              # Fetch from ipinfo.io/ip and echo it
-              run: |
-                  if [[ "$RUNNER_OS" == "Windows" ]]; then
-                    echo "Windows runner IP: $(curl -s https://ipinfo.io/ip)"
-                  elif [[ "$RUNNER_OS" == "macOS" ]]; then
-                    echo "macOS runner IP: $(curl -s https://ipinfo.io/ip)"
-                  else
-                    echo "Linux runner IP: $(curl -s https://ipinfo.io/ip)"
-                  fi
-
-            - name: "Run nox"
-              run: |
-                  # Unit tests
-                  python -m nox -s script_tests --verbose -x -- -xvv
-
-            # - name: "Upload coverage data"
-            #   uses: actions/upload-artifact@v4
-            #   with:
-            #       name: covdata
-            #       path: .coverage.*
+#    documentation_tests:
+#        name: "Documentation testing on ${{ matrix.os }}"
+#        runs-on: "${{ matrix.os }}"
+#
+#        strategy:
+#            fail-fast: false
+#            matrix:
+#                os:
+#                    - ubuntu-latest
+#                    - macos-latest
+#
+#        steps:
+#            - name: "Check out the repo"
+#              uses: "actions/checkout@v4"
+#
+#            - name: "Set up Python"
+#              uses: "actions/setup-python@v5"
+#              with:
+#                  python-version: |
+#                    3.10
+#                    3.11
+#                    3.12
+#
+#            - name: "Install dependencies"
+#              run: |
+#                  python -m pip install --upgrade pip
+#                  python -m pip install nox poetry
+#                  poetry self add poetry-plugin-export
+#
+#            - name: "Get public IP address of runner"
+#              # Need to handle this for Windows, MacOS, and linux
+#              # Fetch from ipinfo.io/ip and echo it
+#              run: |
+#                  if [[ "$RUNNER_OS" == "Windows" ]]; then
+#                    echo "Windows runner IP: $(curl -s https://ipinfo.io/ip)"
+#                  elif [[ "$RUNNER_OS" == "macOS" ]]; then
+#                    echo "macOS runner IP: $(curl -s https://ipinfo.io/ip)"
+#                  else
+#                    echo "Linux runner IP: $(curl -s https://ipinfo.io/ip)"
+#                  fi
+#
+#            - name: "Run nox"
+#              run: |
+#                  # Unit tests
+#                  python -m nox -s script_tests --verbose -x -- -xvv
+#
+#            # - name: "Upload coverage data"
+#            #   uses: actions/upload-artifact@v4
+#            #   with:
+#            #       name: covdata
+#            #       path: .coverage.*
 
     integration_tests:
         name: "DRAGONS integration testing on ${{ matrix.os }}"

.gitignore

@@ -158,7 +158,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # vscode
 .vscode/

astrodata/testing.py

@@ -1447,7 +1447,7 @@ def get_program_observations():
     raise NotImplementedError
 
 
-def expand_file_range(files: str) -> list[str]:
+def expand_file_range(files: str, extn="") -> list[str]:
     """Expand a range of files into a list of file names.
 
     Arguments
@@ -1457,6 +1457,9 @@ def expand_file_range(files: str) -> list[str]:
 
         ["N20170614S0201", "N20170614S0202", ..., "N20170614S0205"]
 
+    extn : str
+        Extension to add to the filename.  Eg ".fits"
+
     Returns
     -------
     list[str]
@@ -1467,7 +1470,7 @@ def expand_file_range(files: str) -> list[str]:
         file_prep, start = file_prep[: -len(end)], file_prep[-len(end) :]
         start, end = int(start), int(end)
         files = [
-            f"{file_prep}{str(i).zfill(len(str(end)))}"
+            f"{file_prep}{str(i).zfill(len(str(end)))}{extn}"
             for i in range(start, end + 1)
         ]
 

docs/conf.py

@@ -6,6 +6,64 @@
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/master/config
 
+# -- Import sanity check ----------------------------------------------------
+# Guard against a stale or duplicate copy of the package being picked up
+# from PYTHONPATH (or any other entry on sys.path ahead of the repo itself).
+# A stray second copy previously caused a confusing failure deep in
+# sphinx.ext.autodoc.importer.get_class_members:
+#   TypeError: argument of type 'property' is not iterable
+# triggered by sphinx_automodapi's custom `type` attrgetter operating on
+# the wrong/stale `Section` class. Fail fast and clearly instead.
+
+import os
+import sys
+
+_PACKAGE_NAME = "astrodata"
+_EXPECTED_REPO_ROOT = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "..")  # adjust if conf.py moves
+)
+
+
+def _check_import_path():
+    """Verify the package being documented is loaded from this repo.
+
+    Raises
+    ------
+    RuntimeError
+        If the imported package resolves to a location outside the
+        expected repository root, which usually means a stray
+        PYTHONPATH entry (or another sys.path entry) is shadowing the
+        local checkout with a different copy of the package.
+    """
+    try:
+        module = __import__(_PACKAGE_NAME)
+    except ImportError as err:
+        raise RuntimeError(
+            f"Could not import '{_PACKAGE_NAME}' while building docs. "
+            f"Check that it is installed/importable in this environment."
+        ) from err
+
+    module_path = os.path.abspath(module.__file__)
+
+    if not module_path.startswith(_EXPECTED_REPO_ROOT):
+        pythonpath = os.environ.get("PYTHONPATH", "<not set>")
+        raise RuntimeError(
+            f"'{_PACKAGE_NAME}' was imported from an unexpected location:\n"
+            f"    {module_path}\n"
+            f"Expected it to be under:\n"
+            f"    {_EXPECTED_REPO_ROOT}\n"
+            f"This usually means PYTHONPATH (or another sys.path entry) "
+            f"is pointing at a different checkout.\n"
+            f"    PYTHONPATH = {pythonpath}\n"
+            f"    sys.path   = {sys.path}\n"
+            f"Unset PYTHONPATH or remove the offending entry and retry."
+        )
+
+_check_import_path()
+
+# --- End of PYTHONPATH check ------------
+
+
 # The full version, including alpha/beta/rc tags
 from astrodata import __version__
 
@@ -15,7 +73,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "astrodata"
-copyright = "2023-present, NOIRLab/Gemini Observatories"
+copyright = "2026, Association of Universities for Research in Astronomy"
 author = "DRAGONS Team"
 
 # -- General configuration ---------------------------------------------------
@@ -38,7 +96,6 @@
     "sphinx_automodapi.smart_resolver",
 ]
 
-
 # Run doctest when building the docs
 doctest_test_doctest_blocks = "True"
 doctest_show_successes = False
@@ -69,7 +126,8 @@
     "astropy": ("http://docs.astropy.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     # "gemini_instruments": ("https://dragons.readthedocs.io/en/latest/", None),
-    "DRAGONS": ("https://dragons.readthedocs.io/en/stable/", None),
+#    "DRAGONS": ("https://dragons.readthedocs.io/en/stable/", None),
+    "DRAGONS": ("https://dragons.readthedocs.io/en/v4.0.0/", None),
 }
 
 intersphinx_disabled_reftypes = ["*"]