Merge pull request #29 from cds-astro/skymap_io

Feat: adds a Skymap submodule

.github/workflows/bench.yml

@@ -13,10 +13,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        #os: [windows-latest, macOS-latest, ubuntu-latest]
-        #python-version: [3.8, 3.9, 3.10]
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
     - name: "Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}"
       uses: actions/setup-python@v4

.github/workflows/test.yml

@@ -45,8 +45,7 @@ jobs:
            maturin build --release --compatibility manylinux2014
            maturin develop --release
            pip install -r requirements-dev.txt
-           python -m pytest python/cdshealpix/tests/test_nested_healpix.py
-           python -m pytest python/cdshealpix/tests/test_ring_healpix.py
+           python -m pytest -v
            deactivate
            rm -r cdshealpixenv
          done
@@ -96,10 +95,8 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
      # Checkout the project
-     - name: "Checkout branch ${{ github.head_ref }}"
+     - name: "Checkout branch"
        uses: actions/checkout@v4
-       with:
-         ref: ${{ github.head_ref }}
      # Test Rust code
      #- name: Run rust wrapper tests
      #  run: cargo test --verbose -- --nocapture
@@ -125,10 +122,7 @@ jobs:
          # Install dependencies
          pip install -r requirements-dev.txt
          # Run tests
-         cd python
-         python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
-         python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
-         cd ..
+         python -m pytest -v
          # Clean
          #pip freeze > requirements-uninstall.txt
          #pip uninstall -r requirements-uninstall.txt -y
@@ -142,10 +136,8 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       # Checkout the project
-      - name: "Checkout branch ${{ github.head_ref }}"
+      - name: "Checkout branch"
         uses: actions/checkout@v4
-        with:
-          ref: ${{ github.head_ref }}
       # Test Rust code
       #- name: Run rust wrapper tests
       #  run: cargo test --verbose -- --nocapture
@@ -170,20 +162,15 @@ jobs:
           # Install dependencies
           pip install -r requirements-dev.txt
           # Run tests
-          cd python
-          python -m pytest -v "cdshealpix\tests\test_nested_healpix.py"
-          python -m pytest -v "cdshealpix\tests\test_ring_healpix.py"
-          cd ..
+          python -m pytest -v
           deactivate
 
-  # Build the doc and run the tests in the doc (only for python 3.9 on ubuntu)
+  # Build the doc and run the tests in the doc (only for python 3.11 on ubuntu)
   test-doc:
     runs-on: ubuntu-latest
     steps:
-      - name: "Checkout branch ${{ github.head_ref }}"
+      - name: "Checkout branch"
         uses: actions/checkout@v4
-        with:
-          ref: ${{ github.head_ref }}
       - name: "Set up Python 3.11 on Ubuntu"
         uses: actions/setup-python@v4
         with:

.pre-commit-config.yaml

@@ -13,7 +13,6 @@ repos:
     rev: 'v1.10.0'
     hooks:
      - id: python-no-eval
-     - id: rst-backticks
   # For python files
   - repo: https://github.com/psf/black
     # Code style

CHANGELOG.md

@@ -7,6 +7,9 @@
 * new features `box_search` and `zone_search` in `cdshealpix.nested`
 * `cdshaelpix.nested.vertices` can now take depth as a `numpy.ndarray` instead of only
   accepting a single depth
+* new module `skymap` added.
+* read/write, and plot nested all-sky skymaps in the implicit scheme from fits files with
+  `Skymap.from_fits`, `Skymap.from_array`, `Skymap.quick_plot`, and `Skymap.to_fits`
 
 ### Fixed
 
@@ -18,6 +21,10 @@
 * `nested.healpix_to_lonlat`, failed into rust panic for `dx=1` or `dy=1`. This is
   now indicated in the documentation and is catched in a `ValueError` on the python side.
 
+### Changed
+
+* `matplotlib` is now an optional dependency, to plot previews of skymaps.
+
 ## 0.6.5
 
 Released 2023-11-28

Cargo.toml

@@ -20,18 +20,19 @@ name = "cdshealpix"
 crate-type = ["cdylib"]
 
 [dependencies]
-healpix = { package = "cdshealpix", version = "0.6" }
+healpix = { rev="5ab172b4d1d206c973f9f170b14509f4982e0090", package = "cdshealpix", git = 'https://github.com/cds-astro/cds-healpix-rust' }
+mapproj = "0.3.0"
 rayon = "1.10"
 
 [dependencies.numpy]
-version = "0.20"
+version = "0.22"
 
 [dependencies.pyo3]
-version = "0.20"
+version = "0.22"
 features = ["extension-module"]
 
 [dependencies.ndarray]
-version = "0.15"
+version = "0.16"
 default-features = false # do not include the default features, and optionally
                          # cherry-pick individual features
 features = ["rayon"]

docs/api.rst

@@ -87,4 +87,14 @@ While in the nested scheme, ``nside`` is a power of two
         vertices
         vertices_skycoord
 
+cdshealpix.skymap
+~~~~~~~~~~~~~~~~~
+
+This module provides a minimal interface to interact with Skymaps, as defined in the
+`data format for gamma ray astronomy specification
+<https://gamma-astro-data-formats.readthedocs.io/en/latest/skymaps/healpix/index.html#skymap-hdu>`_.
+
+.. autoclass:: cdshealpix.skymap.Skymap
+    :members:
+
 .. _cdshealpix: https://github.com/cds-astro/cds-healpix-python

docs/conf.py

@@ -65,6 +65,8 @@
 ]
 default_role = "py:obj"
 numpydoc_class_members_toctree = False
+numpydoc_show_class_members = False
+autosummary_generate = False
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 bibtex_bibfiles = ["references.bib"]

docs/examples/examples.rst

@@ -42,11 +42,23 @@ Zone search
 -----------
 
 In this example, we get the ``ipix`` and ``depth`` in a zone and plot them by combining
-:external:ref:`~cdshealpix.nested.vertices`_ with :external:ref:`~matplotlib.path.Polygon`_
+`cdshealpix.nested.vertices` with `matplotlib.path.Polygon`
 
 .. plot:: examples/search_methods/zone_search.py
     :include-source:
 
+Skymaps
+=======
+
+The skymap sub-module allows to manipulate easily all-sky skymaps in the nested ordering
+and implicit schema.
+The class can be instantiated either from a fits file, with `Skymap.from_fits`, or
+directly with a numpy `numpy.array` containing the values associated to each HEALPix
+pixel.
+
+.. plot:: examples/skymaps/skymaps.py
+    :include-source:
+
 Notebook examples
 =================
 

docs/examples/skymaps/skymaps.py

@@ -0,0 +1,7 @@
+"""Read and plots a quick preview of a skymap in a FITS file."""
+
+from cdshealpix.skymap import Skymap
+
+skymap = Skymap.from_fits("skymap.fits")
+print(skymap.depth)
+skymap.quick_plot()

pyproject.toml

@@ -2,18 +2,31 @@
 [project]
 name = "cdshealpix"
 requires-python = ">=3.8"
-# https://numpy.org/neps/nep-0029-deprecation_policy.html
-# https://docs.astropy.org/en/stable/changelog.html
 dependencies = [
     "astropy<5.3; python_version == '3.8'",
     "astropy; python_version > '3.8'"
 ]
 classifiers = [
     "Programming Language :: Rust",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
+description = "A healpix manipulation library."
+readme = "README.md"
+keywords = ["astronomy", "healpix"]
+
+[project.optional-dependencies]
+plot = ["matplotlib"]
 
 [project.urls]
 repository = "https://github.com/cds-astro/cds-healpix-python"
+documentation = "https://cds-astro.github.io/cds-healpix-python/"
+issues = "https://github.com/cds-astro/cds-healpix-python/issues"
+changelog = "https://github.com/cds-astro/cds-healpix-python/blob/master/CHANGELOG.md"
+
 
 # Build a cdshealpix-x.x.x.tar.gz containing sources (from maturin).
 [build-system]
@@ -44,7 +57,7 @@ output-format = "grouped"
 show-source = true
 ignore-init-module-imports = true
 target-version = "py37"
-extend-select = ["SIM", "D", "UP", "N", "S", "B", "A", "C4", "ICN", "RET", "ARG", "PD", "PGH", "RUF"]
+extend-select = ["SIM", "D", "UP", "N", "S", "B", "A", "C4", "ICN", "RET", "ARG", "PGH", "RUF"]
 extend-ignore = ["E501"]
 # E501: line length (done by black in our case)
 exclude = ["conf.py"]
@@ -67,6 +80,6 @@ max-string-length = 20
 convention = "numpy"  # Accepts: "google", "numpy", or "pep257"
 
 [tool.pytest.ini_options]
-addopts = "--doctest-modules"
+addopts = "--doctest-modules --ignore-glob=python/cdshealpix/tests/test_bench*"
 doctest_optionflags = "NORMALIZE_WHITESPACE"
 testpaths = "python"

python/cdshealpix/skymap/__init__.py

@@ -0,0 +1 @@
+from .skymap import Skymap  # noqa: F401