Merge branch 'main' into dysh_data2

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
@@ -63,7 +63,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
           cache: pip
       - run: pip install --upgrade coverage[toml]
       - uses: actions/download-artifact@v4

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
     - name: Set up Python ubuntu-latest
       uses: actions/setup-python@v4
       with:
-        python-version: '3.9'  # Should always be the minimum supported Python version
+        python-version: '3.10'  # Should always be the minimum supported Python version
         cache: 'pip'
         cache-dependency-path': 'requirements.txt'
     - name: Install dependencies

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 ---
 # See https://pre-commit.com for more information
 default_language_version:
-  python: python3.9
+  python: python3.10
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: 'https://github.com/pre-commit/pre-commit-hooks'
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: '(notebooks|attic|benchmark|testdata)/.*'
@@ -30,7 +30,7 @@ repos:
       - id: isort
         exclude: '(notebooks|attic|benchmark|testdata)/.*'
   - repo: 'https://github.com/psf/black'
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         exclude: '(notebooks|attic|benchmark|testdata)/.*'

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
     os: ubuntu-22.04
     tools:
-        python: "3.9"
+        python: "3.10"
         # You can also specify other tool versions:
         # nodejs: "19"
         # rust: "1.64"

docs/source/_static/css/custom.css

@@ -1,11 +1,95 @@
 /* Remove width restriction on content so that diagrams
-   are more visible */
-   .wy-nav-content {
-      max-width: none;
-  }
-
-  /* Override the logo/searchbar background color;
-     it conflicts with the logo color */
-  .wy-side-nav-search {
-      background-color: #C6B9D2;
-  }
+are more visible */
+.wy-nav-content {
+  max-width: none;
+}
+
+/* Override the logo/searchbar background color;
+ it conflicts with the logo color */
+.wy-side-nav-search {
+  background-color: #C6B9D2;
+}
+
+.black {
+    color: black;
+}
+
+.gray {
+    color: gray;
+}
+
+.grey {
+    color: gray;
+}
+
+.silver {
+    color: silver;
+}
+
+.white {
+    color: white;
+}
+
+.maroon {
+    color: maroon;
+}
+
+.red {
+    color: red;
+}
+
+.magenta {
+    color: magenta;
+}
+
+.fuchsia {
+    color: fuchsia;
+}
+
+.pink {
+    color: pink;
+}
+
+.orange {
+    color: orange;
+}
+
+.yellow {
+    color: yellow;
+}
+
+.lime {
+    color: lime;
+}
+
+.green {
+    color: green;
+}
+
+.olive {
+    color: olive;
+}
+
+.teal {
+    color: teal;
+}
+
+.cyan {
+    color: cyan;
+}
+
+.aqua {
+    color: aqua;
+}
+
+.blue {
+    color: blue;
+}
+
+.navy {
+    color: navy;
+}
+
+.purple {
+    color: purple;
+}

docs/source/conf.py

@@ -58,6 +58,7 @@
     "sphinxcontrib.mermaid",
     "numpydoc",
     "sphinx_inline_tabs",
+    "sphinx_design",
 ]
 
 numpydoc_show_class_members = True
@@ -75,6 +76,11 @@
 # TODO: These appear to have no effect
 mermaid_verbose = True
 
+# Mermaid configuration
+# https://github.com/mgaitan/sphinxcontrib-mermaid
+mermaid_version = "11.2.0"
+mermaid_params = ["--theme", "dark"]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -101,7 +107,7 @@
 # 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 = []
+exclude_patterns = ["examples/output"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
@@ -120,11 +126,25 @@
 # documentation.
 #
 html_theme_options = {
+    "repository_url": "https://github.com/GreenBankObservatory/dysh",
+    "repository_branch": "main",
     "logo": {
         "image_light": "_static/icon/dysh_logo_lightmode.png",
         "image_dark": "_static/icon/dysh_logo_darkmode.png",
     },
+    # "show_toc_level": 2,
+    "use_source_button": True,
+    "use_issues_button": True,
+    "use_download_button": True,
+    "use_sidenotes": True,
     "show_toc_level": 2,
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/GreenBankObservatory/dysh",
+            "icon": "fa-brands fa-github",
+        },
+    ],
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/source/explanations/index.rst

@@ -0,0 +1,58 @@
+.. _explanations:
+
+###############################################
+:octicon:`repo;2em;purple` Explanation Material
+###############################################
+
+Big-picture explanations of higher-level concepts. Most useful for building understanding of a particular topic.
+
+dysh
+====
+
+.. grid:: 1 2 2 2
+
+    .. grid-item-card::
+        :shadow: md
+        :margin: 2 2 0 0
+
+        :octicon:`container;3em;green` **ScanBlock**
+
+        What is a ScanBlock?
+
+        .. button-link:: scanblock/index.html
+            :color: primary
+            :tooltip: Details of what is a ScanBlock
+            :outline:
+            :click-parent:
+
+            ScanBlock
+
+
+SDFITS
+======
+
+.. grid:: 1 2 2 2
+
+    .. grid-item-card::
+        :shadow: md
+        :margin: 2 2 0 0
+
+        :octicon:`file;3em;green` **SDFITS**
+
+        What are SDFITS files?
+
+        .. button-link:: sdfits/index.html
+            :color: primary
+            :tooltip: SDFITS details
+            :outline:
+            :click-parent:
+
+            SDFITS
+
+
+.. toctree::
+    :hidden:
+    :maxdepth: 3
+
+    scanblock/index
+    sdfits/index

docs/source/explanations/scanblock/index.rst

@@ -0,0 +1,42 @@
+.. _scanblocks:
+
+#########
+ScanBlock
+#########
+
+.. mermaid::
+
+    flowchart TD
+
+    subgraph newLines[GBTFITSLoad
+        50 Scans
+        Position Switching
+        Dual Linear Polarization
+        1 Beam
+        4 Frequency Windows
+        100 integrations each
+        ]
+
+
+
+
+    end
+
+
+    newLines -- getps( scan=45, plnum=1, ifnum=0 ) --> ScanBlock1
+    newLines -- gettp( scan=[17,18,19], intnum=np.r_[50:100], ifnum=2 ) --> ScanBlock2
+
+
+
+    subgraph ScanBlock1[ScanBlock]
+            psscan["spectra.scan.PSScan<br />scans = 44,45<br />plnum = 1<br />ifnum = 0<br />intnum = (0,100)"]
+        end
+    subgraph ScanBlock2[ScanBlock]
+            tpscan1["spectra.scan.TPScan<br />scan=17<br />plnum = 0<br />ifnum = 2<br />intnum=(50,100)"]
+            tpscan2["spectra.scan.TPScan<br />scan=18<br />plnum = 0<br />ifnum = 2<br />intnum=(50,100)"]
+            tpscan3["spectra.scan.TPScan<br />scan=19<br />plnum = 0<br />ifnum = 2<br />intnum=(50,100)"]
+
+        end
+
+    ScanBlock1[Scan Block] -- timeaverage() --->spectrum1[Spectrum]
+    ScanBlock2[Scan Block] -- timeaverage() --->spectrum2[Spectrum]

docs/source/explanations/sdfits/index.rst

@@ -0,0 +1,7 @@
+.. _sdfits-explanation:
+
+############
+SDFITS Files
+############
+
+This section is empty for now, but you can check the column definitions :ref:`here <sdfits-reference>`, or the SDFITS convention as defined in `AIPS++ <https://casa.nrao.edu/aips2_docs/notes/236/node14.html>`_ or at `ADASS IX <https://www.aspbooks.org/a/volumes/article_details/?paper_id=20663>`_, or `the registered SDFITS convention <https://fits.gsfc.nasa.gov/registry/sdfits.html>`_.

docs/source/for_beta_testers/beta_testing.rst

@@ -70,7 +70,7 @@ We provide steps for working in one of `GBO data reduction hosts <https://greenb
 
 .. tab:: Outside of GBO
 
-    Create a `Python3.9+` virtual environment
+    Create a `Python3.10+` virtual environment
 
     .. code:: bash
 

docs/source/for_developers/git_workflows.rst

@@ -55,6 +55,7 @@ In the directory you want to work in, set up the repo:
 To check out a branch called {{branch-name}}, just do
 
 .. code-block:: bash
+
     $ git checkout {{branch-name}}
 
 Current development is done in the `main` branch. To set up your own development branch called `{{your-name}}-devel`, do the following: