nikamap 1.2.2__tar.gz → 1.4.dev0__tar.gz

{nikamap-1.2.2 → nikamap-1.4.dev0}/.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/OpenAstronomy/packaging-guide",
-  "commit": "ad6da17e1d8fd96456566abed30b510bf8b5f8c8",
+  "commit": "d4aa2e8806bf57505dc65793009bd9ecb2777364",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -24,7 +24,8 @@
         "docs/_static",
         ".github/workflows/sub_package_update.yml"
       ],
-      "_template": "https://github.com/OpenAstronomy/packaging-guide"
+      "_template": "https://github.com/OpenAstronomy/packaging-guide",
+      "_commit": "d4aa2e8806bf57505dc65793009bd9ecb2777364"
     }
   },
   "directory": null

nikamap-1.4.dev0/.gitattributes

@@ -0,0 +1,4 @@
+*.fits filter=lfs diff=lfs merge=lfs -text
+doc/auto_examples/**/*.zip filter=lfs diff=lfs merge=lfs -text
+doc/auto_examples/**/*.ipynb filter=lfs diff=lfs merge=lfs -text
+doc/auto_examples/**/*.png filter=lfs diff=lfs merge=lfs -text

{nikamap-1.2.2 → nikamap-1.4.dev0}/.github/workflows/sub_package_update.yml

@@ -37,7 +37,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 

{nikamap-1.2.2 → nikamap-1.4.dev0}/.gitignore

@@ -160,7 +160,8 @@ cython_debug/
 #.idea/
 
 _build/
-auto_examples/
+# auto_examples/ is committed (pre-built) so that RTD can serve it without re-executing
+# auto_examples/
 gen_api/
 reports/
 .vscode/

{nikamap-1.2.2 → nikamap-1.4.dev0}/.gitlab-ci.yml

@@ -123,11 +123,22 @@ ruff:
       - ".cache/pip"
       - ".ruff_cache"
 
-#pages:
-#  script:
-#    - pip install sphinx sphinx-rtd-theme
-#    - cd doc ; make html
-#    - mv build/html/ ../public/
+# ---------------------------------------------------------------------------
+# GitLab Pages — build and publish the Sphinx documentation automatically.
+# The HTML output is available at https://<namespace>.gitlab.io/<project>/
+# Triggered on every push to the default branch and on tags.
+# ---------------------------------------------------------------------------
+pages:
+  stage: deploy
+  script:
+    - pip install --quiet ".[docs]"
+    - sphinx-build -b html doc public --keep-going
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+    - if: $CI_COMMIT_TAG
 #  artifacts:
 #    paths:
 #      - public

nikamap-1.4.dev0/.readthedocs.yaml

@@ -0,0 +1,34 @@
+# .readthedocs.yaml — Read the Docs v2 configuration (required as of 2024)
+# Docs: https://docs.readthedocs.io/en/stable/config-file/v2.html
+#
+# To activate automatic builds from GitLab:
+#   1. Go to https://readthedocs.org and log in with your GitLab account (OAuth).
+#   2. Click "Import a Project" → select this repository.
+#   3. RTD will automatically add a webhook on the GitLab side.
+#   4. Every push to the default branch (and every tag) will trigger a new build.
+
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.11"
+  apt_packages:
+    - git-lfs
+  jobs:
+    post_system_dependencies:
+      # git-lfs is now installed via apt_packages; download LFS objects
+      - git lfs install
+      - git lfs pull
+
+python:
+  install:
+    # Install the package with its documentation dependencies
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  configuration: doc/conf.py
+  fail_on_warning: false

{nikamap-1.2.2 → nikamap-1.4.dev0}/CHANGELOG.md

@@ -7,6 +7,21 @@ Added
 Fixed
 -----
 
+Version 1.3
+===========
+
+Added
+-----
+* New `ContMap.simstack` method: supports linear regression-based stacking (SimStack) for multiple source groups, with error estimation. [Viero et al. 2013]
+* New `stack.py` module: all stacking logic (including cutout, reproject, and simstack) is now modularized in StackMixin.
+* Dedicated and parameterized tests for stacking and simstack in `tests/test_stack.py`.
+
+Fixed
+-----
+* Refactored and cleaned up stacking code: removed legacy stacking routines from `contmap.py`, improved maintainability and testability.
+* Harmonized position generation utilities (`pos_uniform`, `pos_uniform_no_overlap`, etc.).
+* Improved robustness of WCS-related functions; extended tests to cover fit uncertainty.
+
 Version 1.2.2
 =============
 

nikamap-1.4.dev0/CONTRIBUTING.rst

@@ -0,0 +1,119 @@
+Contributing to nikamap
+=======================
+
+Thank you for contributing to ``nikamap``.
+
+This project provides tools to read and analyse NIKA2 continuum maps. Contributions
+that improve scientific correctness, package stability, documentation, and test
+coverage are all useful.
+
+Ways to contribute
+------------------
+
+You can contribute by:
+
+- reporting bugs or regressions;
+- proposing or implementing new features;
+- improving tests;
+- clarifying documentation and examples;
+- improving compatibility with supported Python, Astropy, and Photutils versions.
+
+Before opening a change, check whether a similar issue or merge request already exists.
+When you report a bug, include the package version, Python version, and a minimal example
+that reproduces the problem.
+
+Development setup
+-----------------
+
+``nikamap`` requires Python 3.10 or later.
+
+1. Clone the repository.
+2. Create and activate a virtual environment.
+3. Install the package in editable mode with the development extras you need.
+
+Example:
+
+.. code:: bash
+
+    python -m venv .venv
+    source .venv/bin/activate
+    python -m pip install --upgrade pip
+    python -m pip install -e ".[test,docs]"
+
+The optional ``stacking`` extra can also be installed when working on reprojection-related
+features:
+
+.. code:: bash
+
+    python -m pip install -e ".[test,docs,stacking]"
+
+Running tests
+-------------
+
+For a quick local test run:
+
+.. code:: bash
+
+    pytest --pyargs nikamap
+
+The repository also defines a tox matrix to test multiple Python and Photutils combinations:
+
+.. code:: bash
+
+    tox -e py311-photutils230
+
+You can list the available environments in ``tox.ini``. When fixing a compatibility issue,
+prefer running the tox environment that matches the affected dependency combination.
+
+
+Linting with Ruff
+-----------------
+
+Ruff is run in CI (GitLab job ``ruff``) and should be clean for contributions.
+Run it locally before opening a merge request:
+
+.. code:: bash
+
+    python -m pip install ruff
+    ruff check .
+
+To automatically fix what Ruff can fix safely:
+
+.. code:: bash
+
+    ruff check . --fix
+
+Documentation
+-------------
+
+The documentation sources live in ``doc/`` and examples are under ``examples/``.
+To build the HTML documentation locally:
+
+.. code:: bash
+
+    tox -e build_docs
+
+If your change modifies public behaviour, update the relevant documentation and examples.
+
+Code and test expectations
+--------------------------
+
+- Keep changes focused and avoid unrelated refactors.
+- Follow the existing coding style in the modified files.
+- Add or update tests for behaviour changes and bug fixes.
+- Preserve scientific metadata when applicable, especially units, WCS information, and beam handling.
+- Be mindful of compatibility with the supported Photutils versions exercised by ``tox``.
+
+Submitting changes
+------------------
+
+When opening a contribution, include:
+
+- a short description of the problem being solved;
+- the approach taken;
+- any limitations or follow-up work;
+- test coverage for the change.
+
+If the change affects users, update ``CHANGELOG.md`` when appropriate.
+
+Small, well-scoped contributions are easier to review and merge.

{nikamap-1.2.2/nikamap.egg-info → nikamap-1.4.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nikamap
-Version: 1.2.2
+Version: 1.4.dev0
 Summary: nikamap: a package to manipulate data produced by the IDL NIKA2 pipeline
 Author-email: Alexandre Beelen <alexandre.beelen@lam.fr>
 License: The MIT License (MIT)
@@ -48,7 +48,6 @@ Requires-Dist: pytest-doctestplus; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-mpl; extra == "test"
 Requires-Dist: reproject; extra == "test"
-Requires-Dist: setuptools_scm>=6.2; extra == "test"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinx-automodapi; extra == "docs"
@@ -61,7 +60,28 @@ NikaMap
 =======
 |pypi| |license| |wheels| |format| |pyversions| |rtd|
 
-`nikamap` is a python package to manipulate data produced by the IDL or PIIC NIKA2 pipeline.
+`nikamap` is a Python package built around `ContMap`, a general-purpose class
+for processing and analysing continuum maps from radio/millimetre
+observatories.  It provides beam handling, match-filtering, point-source
+detection and photometry, and cutout / simultaneous stacking.
+
+For NIKA2 users, `nikamap` offers first-class support for the FITS data
+products of both the **IDL** and **PIIC** NIKA2 reduction pipelines through
+`NikaMap` and `NikaFits`, thin subclasses of `ContMap` that handle
+multi-band files and scan-level jackknife realisations.
+
+Quick start with generic continuum data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code:: python
+
+    from nikamap import ContMap
+
+    cm = ContMap.read('mymap.fits')
+    cm.plot()
+
+Quick start with NIKA2 data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code:: python
 
@@ -70,11 +90,11 @@ NikaMap
     nm = NikaMap.read('map.fits', band='1mm')
     nm.plot()
 
-or alternatively
+or using the multi-band container:
 
 .. code:: python
 
-   from nikamap import NikaFits
+    from nikamap import NikaFits
 
     data = NikaFits.read('map.fits')
     data['1mm'].plot()
@@ -177,31 +197,5 @@ This project is licensed under the MIT license.
 Contributing
 ------------
 
-We love contributions! cruft_openastro is open source,
-built on open source, and we'd love to have you hang out in our community.
-
-**Imposter syndrome disclaimer**: We want your help. No, really.
-
-There may be a little voice inside your head that is telling you that you're not
-ready to be an open source contributor; that your skills aren't nearly good
-enough to contribute. What could you possibly offer a project like this one?
-
-We assure you - the little voice in your head is wrong. If you can write code at
-all, you can contribute code to open source. Contributing to open source
-projects is a fantastic way to advance one's coding skills. Writing perfect code
-isn't the measure of a good developer (that would disqualify all of us!); it's
-trying to create something, making mistakes, and learning from those
-mistakes. That's how we all improve, and we are happy to help others learn.
-
-Being an open source contributor doesn't just mean writing code, either. You can
-help out by writing documentation, tests, or even giving feedback about the
-project (and yes - that includes giving feedback about the contribution
-process). Some of these contributions may be the most valuable to the project as
-a whole, because you're coming to the project with fresh eyes, so you can see
-the errors and assumptions that seasoned contributors have glossed over.
-
-Note: This disclaimer was originally written by
-`Adrienne Lowe <https://github.com/adriennefriend>`_ for a
-`PyCon talk <https://www.youtube.com/watch?v=6Uj746j9Heo>`_, and was adapted by
-cruft_openastro based on its use in the README file for the
-`MetPy project <https://github.com/Unidata/MetPy>`_.
+See ``CONTRIBUTING.rst`` for the development setup, test commands, documentation build,
+and contribution expectations.

{nikamap-1.2.2 → nikamap-1.4.dev0}/README.rst

@@ -2,7 +2,28 @@ NikaMap
 =======
 |pypi| |license| |wheels| |format| |pyversions| |rtd|
 
-`nikamap` is a python package to manipulate data produced by the IDL or PIIC NIKA2 pipeline.
+`nikamap` is a Python package built around `ContMap`, a general-purpose class
+for processing and analysing continuum maps from radio/millimetre
+observatories.  It provides beam handling, match-filtering, point-source
+detection and photometry, and cutout / simultaneous stacking.
+
+For NIKA2 users, `nikamap` offers first-class support for the FITS data
+products of both the **IDL** and **PIIC** NIKA2 reduction pipelines through
+`NikaMap` and `NikaFits`, thin subclasses of `ContMap` that handle
+multi-band files and scan-level jackknife realisations.
+
+Quick start with generic continuum data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code:: python
+
+    from nikamap import ContMap
+
+    cm = ContMap.read('mymap.fits')
+    cm.plot()
+
+Quick start with NIKA2 data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code:: python
 
@@ -11,11 +32,11 @@ NikaMap
     nm = NikaMap.read('map.fits', band='1mm')
     nm.plot()
 
-or alternatively
+or using the multi-band container:
 
 .. code:: python
 
-   from nikamap import NikaFits
+    from nikamap import NikaFits
 
     data = NikaFits.read('map.fits')
     data['1mm'].plot()
@@ -118,31 +139,5 @@ This project is licensed under the MIT license.
 Contributing
 ------------
 
-We love contributions! cruft_openastro is open source,
-built on open source, and we'd love to have you hang out in our community.
-
-**Imposter syndrome disclaimer**: We want your help. No, really.
-
-There may be a little voice inside your head that is telling you that you're not
-ready to be an open source contributor; that your skills aren't nearly good
-enough to contribute. What could you possibly offer a project like this one?
-
-We assure you - the little voice in your head is wrong. If you can write code at
-all, you can contribute code to open source. Contributing to open source
-projects is a fantastic way to advance one's coding skills. Writing perfect code
-isn't the measure of a good developer (that would disqualify all of us!); it's
-trying to create something, making mistakes, and learning from those
-mistakes. That's how we all improve, and we are happy to help others learn.
-
-Being an open source contributor doesn't just mean writing code, either. You can
-help out by writing documentation, tests, or even giving feedback about the
-project (and yes - that includes giving feedback about the contribution
-process). Some of these contributions may be the most valuable to the project as
-a whole, because you're coming to the project with fresh eyes, so you can see
-the errors and assumptions that seasoned contributors have glossed over.
-
-Note: This disclaimer was originally written by
-`Adrienne Lowe <https://github.com/adriennefriend>`_ for a
-`PyCon talk <https://www.youtube.com/watch?v=6Uj746j9Heo>`_, and was adapted by
-cruft_openastro based on its use in the README file for the
-`MetPy project <https://github.com/Unidata/MetPy>`_.
+See ``CONTRIBUTING.rst`` for the development setup, test commands, documentation build,
+and contribution expectations.

{nikamap-1.2.2 → nikamap-1.4.dev0}/doc/_templates/class.rst

@@ -4,7 +4,9 @@
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
+   :members:
    :special-members: __contains__,__getitem__,__iter__,__len__,__add__,__sub__,__mul__,__div__,__neg__,__hash__
+   :member-order: bysource
 
 .. include:: {{module}}.{{objname}}.examples
 

{nikamap-1.2.2 → nikamap-1.4.dev0}/doc/api.rst

@@ -1,6 +1,10 @@
 API
 ===
 
+The autogenerated API reference below is complemented by the
+:doc:`contmap` guide, which highlights the map analysis and stacking
+workflows most commonly used in practice.
+
 
 Classes
 -------

nikamap-1.4.dev0/doc/auto_examples/G2/bootstrap.codeobj.json

@@ -0,0 +1,38 @@
+{
+ ":class:": [
+  {
+   "is_class": false,
+   "is_explicit": true,
+   "module": "builtins",
+   "module_short": "builtins",
+   "name": ":class:"
+  }
+ ],
+ "Bootstrap": [
+  {
+   "is_class": false,
+   "is_explicit": false,
+   "module": "nikamap",
+   "module_short": "nikamap",
+   "name": "Bootstrap"
+  }
+ ],
+ "Path": [
+  {
+   "is_class": false,
+   "is_explicit": false,
+   "module": "pathlib",
+   "module_short": "pathlib",
+   "name": "Path"
+  }
+ ],
+ "nikamap.analysis.Bootstrap": [
+  {
+   "is_class": false,
+   "is_explicit": true,
+   "module": "nikamap.analysis",
+   "module_short": "nikamap",
+   "name": "Bootstrap"
+  }
+ ]
+}

nikamap-1.4.dev0/doc/auto_examples/G2/bootstrap.ipynb

@@ -0,0 +1,122 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Bootstraping error\n\nSimple example of bootstrap on G2 dataset from the N2CLS GTO.\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "First import the :class:`nikamap.analysis.Bootstrap` class\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "from pathlib import Path\nfrom nikamap import Bootstrap"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "This define the root directory where all the data ...\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "DATA_DIR = Path(\"/data/NIKA/Reduced/G2_COMMON_MODE_ONE_BLOCK/v_1\")"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "can be retrieved using a simple regular expression\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "filenames = list(DATA_DIR.glob(\"*/map.fits\"))\nfilenames"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Generate a bootstrap dataset for all the maps.\n\n<div class=\"alert alert-info\"><h4>Note</h4><p>At the moment, this is very memory demanding as we use\n          ```map_size * (len(filenames) + n_bootstrap))```</p></div>\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "nm = Bootstrap(filenames, n_bootstrap=200, ipython_widget=True)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "In the resulting :class:`nikamap.NikaMap` object, the uncertainty as been computed using the bootstrap technique.\n\n<div class=\"alert alert-danger\"><h4>Warning</h4><p>The resulting uncertainty map could still be biased, see https://gitlab.lam.fr/N2CLS/NikaMap/issues/4</p></div>\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "_ = nm.plot_SNR(cbar=True)"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.11.15"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}