Release 1.1 to main

.github/ISSUE_TEMPLATE/bug_report.md

@@ -14,6 +14,9 @@ What is the bug? What did you expect to happen vs. what actually happened?
 Include a minimal example that reproduces your issue. This should probably be a brief snippet of Python code along with a traceback. Please format [using triple backticks](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax#quoting-code).
 
 **Environment**
-- Dysh version
+Please provide the outputs of ``dysh.system_info()`` here (only available after dysh 1.1.0).
+To get the outputs use: ``dysh -s``.
+If using dysh<=1.1.0 provide:
+- dysh version
 - Python version
 - OS

.github/workflows/ci-latest-deps.yml

@@ -9,6 +9,7 @@ env:
   FORCE_COLOR: '1'
   MPLBACKEND: Agg
   QT_QPA_PLATFORM: offscreen
+  DYSH_DATA: ${{ github.workspace }}/.dysh_cache
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
@@ -27,9 +28,11 @@ jobs:
           - os: windows-latest
             python-version: '3.13'
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           version: 0.9.17
           python-version: ${{ matrix.python-version }}
@@ -38,6 +41,11 @@ jobs:
         run: uv sync -U --all-extras --dev
       - name: Log resolved dependency versions
         run: uv pip list
+      - name: Cache example data
+        uses: actions/cache@v5
+        with:
+          path: ${{ github.workspace }}/.dysh_cache
+          key: dysh-example-data-v1
       - name: Test with pytest
         run: |
           uv run pytest --numprocesses auto -m "not gbo_only" --timeout=0
@@ -49,7 +57,7 @@ jobs:
       issues: write
     steps:
       - name: Create or update failure issue
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           script: |
             const title = 'CI (Latest Deps) is failing';

.github/workflows/ci.yml

@@ -16,6 +16,7 @@ env:
   FORCE_COLOR: '1' # Make tools pretty.
   MPLBACKEND: Agg # hard-force headless backend (tkagg bad!)
   QT_QPA_PLATFORM: offscreen # No real display. Renders to memory. Not sure if Qt ever gets pulled in though
+  DYSH_DATA: ${{ github.workspace }}/.dysh_cache
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
@@ -26,15 +27,22 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           version: 0.9.17 # Update this occasionally to stay up to date!
           python-version: ${{ matrix.python-version }}
           enable-cache: true
       - name: Install the project
         run: uv sync --all-extras --dev
+      - name: Cache example data
+        uses: actions/cache@v5
+        with:
+          path: ${{ github.workspace }}/.dysh_cache
+          key: dysh-example-data-v1
       - name: Test with pytest
         env:
           COVERAGE_FILE: coverage.${{ matrix.os }}.${{ matrix.python-version }}
@@ -45,7 +53,7 @@ jobs:
       - name: Upload coverage data
         # Upload only ubuntu results, since we are only running the coverage step on ubuntu
         if: matrix.os == 'ubuntu-latest'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: coverage.${{ matrix.os }}.${{ matrix.python-version }}
           path: coverage.ubuntu-latest*
@@ -54,9 +62,11 @@ jobs:
     runs-on: ubuntu-latest
     continue-on-error: true
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           version: 0.9.17
           python-version: '3.13'
@@ -65,22 +75,29 @@ jobs:
         run: uv sync -U --all-extras --dev
       - name: Log resolved dependency versions
         run: uv pip list
+      - name: Cache example data
+        uses: actions/cache@v5
+        with:
+          path: ${{ github.workspace }}/.dysh_cache
+          key: dysh-example-data-v1
       - name: Test with pytest
         run: |
           uv run pytest --numprocesses auto -m "not gbo_only" --timeout=0
   coverage:
     needs: tests
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           version: 0.9.17 # Update this occasionally to stay up to date!
           enable-cache: true
       - name: Install the project
         run: uv sync --all-extras --dev
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           pattern: coverage.*
           path: coverage-data
@@ -96,7 +113,7 @@ jobs:
           # Report again and fail if under 100%.
           # coverage report --fail-under=100
       - name: Upload HTML report
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: html-report
           path: htmlcov

.github/workflows/release.yml

@@ -12,9 +12,9 @@ jobs:
       # See: https://github.com/pypa/gh-action-pypi-publish#trusted-publishing
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           version: 0.8.19 # Update this occasionally to stay up to date!
           python-version: '3.10'

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
     hooks:
       - id: yamlfmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.15.12
     hooks:
       - id: ruff-format
       - id: ruff-check

.readthedocs.yaml

@@ -7,7 +7,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.11"
   jobs:
     create_environment:
       - asdf plugin add uv

docs/source/conf.py

@@ -16,6 +16,8 @@
 
 sys.path.insert(0, os.path.abspath("../../src"))
 sys.path.insert(0, os.path.abspath("."))
+# Detect a real Read the Docs build before we overwrite the variable below.
+ON_RTD = os.environ.get("READTHEDOCS") == "True"
 os.environ["READTHEDOCS"] = "True"  # Fool dysh to use StaticLabGUI.
 print(f"Are we fooling anyone? {os.environ['READTHEDOCS']}")
 
@@ -108,7 +110,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ["examples/output"]
+exclude_patterns = ["examples/output", "_build", "**.ipynb_checkpoints"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
@@ -266,12 +268,12 @@
 
 # Settings for myst_nb notebook rendering
 
-# Cache notebooks to only re-run when cells change.
-nb_execution_mode = "cache"
+# On Read the Docs, skip execution and render the outputs saved in the
+# notebooks (executing all of them exceeds the RTD build timeout).
+# Locally, cache notebooks to only re-run when cells change.
+nb_execution_mode = "off" if ON_RTD else "cache"
 # Use this mode if working on the documentation with sphinx-autobuild.
 # nb_execution_mode = "auto"
-# Use this to skip executing the notebooks.
-# nb_execution_mode = "off"
 
 # Execution timeout.
 # -1 should set this to no limit.

docs/source/index.rst

@@ -39,6 +39,10 @@ After being installed, the ``dysh`` command will be available through the comman
 This will launch an `iPython <https://ipython.readthedocs.io/en/stable/>`_ session with some modules and classes pre-loaded (e.g., `~dysh.fits.gbtfitsload.GBTFITSLoad`), and with logging.
 We refer to this interface as the dysh shell.
 
+.. note::
+
+   For large SDFITS files (> 1 GB or so), dysh may create temporary files during certain operations to hold flag arrays.  By default these files are created in ``/tmp``. To avoid filling up ``/tmp``, you can (and should) change that default by setting ``$DYSH_SCRATCH`` or ``$TMPDIR`` environment variables to point to a directory where temporary files can be written.  Note these must be set before you start dysh as the values are cached by Python at startup, so ``os.putenv()`` would not have any effect..
+
 Loading Data
 ============
 
@@ -153,6 +157,41 @@ Plot again, but focus on the line-free regions:
 
 .. image:: files/spectrum_plot_bsub.png
 
+
+Using Exclude Regions
+--------------------------------
+
+When you give an ``exclude`` value to ``baseline``, the default behavior is to store it in the `exclude_regions <dysh.spectra.spectrum.Spectrum.exclude_regions>` property, which is a list of `SpectralRegions <astropy.coordinate.SpectralRegion>`.   Subsequent baseline operations on the spectrum can reuse these exclude regions, append to them, or ignore them, depending on the value of the ``exclude_action`` keyword. Options are:
+
+        - "replace" : replace the `Spectrum.exclude_regions` list with the input region.
+        - "append" : append the input region to the `Spectrum.exclude_regions` list.
+        - None      : Use the the input region, but do not change the existing `Spectrum.exclude_regions`
+
+
+The default is "replace."   Below is example usage.
+
+.. code:: Python
+
+    s = Spectrum.fake_spectrum(1024)
+    exclude1 = [(1,100)]
+    exclude2 = [(924,1024)]
+
+    # The input exclude regions are used in the baseline and are stored in the Spectrum.
+    s.baseline(degree=1,exclude=exclude1)
+
+    # The input exclude regions are used and replace the previously stored regions.
+    s.baseline(degree=1,exclude=exclude2)
+
+    # The input exclude regions are appended to the stored regions.
+    s.baseline(degree=1,exclude=exclude1, exclude_action="append")
+
+    # The input exclude regions are used but the stored regions are unaffected.
+    s.baseline(degree=1,exclude=exclude2, exclude_action=None)
+
+    # The input exclude regions are used and replace the previously stored regions.
+    s.baseline(degree=1,exclude=exclude1, exclude_action="replace")
+
+
 Polarization Average
 ====================