Merge branch 'main' into saransh/test_fields

glass-dev · Nov 15, 2024 · 5bb94b3 · 5bb94b3
2 parents 8dc4263 + 0dd2fb9
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -21,6 +21,21 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v4
 
+      - name: Replace stable version with the release version
+        run: |-
+          # store the release tag
+          tag="${{ github.ref_name }}"
+
+          # regex patterns
+          badge_pattern="s#(readthedocs\.org/projects/glass/badge/\?version=)stable#\1${tag}#g"
+          url_pattern="s#(glass\.readthedocs\.io.*?)/stable#\1/${tag}#g"
+
+          # perform the replacements
+          sed --in-place --regexp-extended \
+            --expression "$badge_pattern" \
+            --expression "$url_pattern" \
+            ${{ github.workspace }}/README.md
+
       - name: Build SDist and wheel
         run: pipx run build
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,8 +2,23 @@
 
 # Changelog
 
-All notable changes to the project are documented in this file. The format is
-based on [Keep a Changelog](https://keepachangelog.com).
+All functional changes to the project are documented in this file.
+
+## [2024.2] (15 Nov 2024)
+
+- gh-188: add docstrings to all functions and tidy docs (#381)
+- gh-336: support Python 3.13 (#337)
+- gh-358: add static types support (#368)
+- gh-131: rename `gaussian_gls` to `discretized_cls` (#345)
+- gh-328: efficient resampling in `ellipticity_ryden04` (#341)
+- gh-137: deprecate `redshifts_from_nz` in favor of `redshifts` (#333)
+- gh-328: fix shape mismatch bug in ellipticity_ryden04 (#332)
+- gh-315: add broadcasting rule in ellipticity_ryden04 + tests (#317)
+- gh-198: enforce `python>3.8` & `numpy>1.21` (#326)
+- gh-260: remove glass.core.constants (#261)
+- gh-107: add all public functions/classes under glass namespace (#221)
+- gh-168: move examples into repository (#169)
+- gh-156: add FITS catalogue writer tool (#158)
 
 ## [2024.1] (16 Jul 2024)
 
@@ -143,6 +158,7 @@ based on [Keep a Changelog](https://keepachangelog.com).
 
 - Initial wide release for GLASS paper
 
+[2024.2]: https://github.com/glass-dev/glass/compare/v2024.1...v2024.2
 [2024.1]: https://github.com/glass-dev/glass/compare/v2023.7...v2024.1
 [2023.7]: https://github.com/glass-dev/glass/compare/v2023.6...v2023.7
 [2023.6]: https://github.com/glass-dev/glass/compare/v2023.5...v2023.6

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -78,7 +78,7 @@ rendering documentation on its website. The configuration file (`conf.py`) for
 `sphinx` can be found
 [under the `docs` folder](https://github.com/glass-dev/glass/blob/main/docs/conf.py).
 The documentation is deployed on <https://readthedocs.io>
-[here](https://glass.readthedocs.io/en/latest/).
+[here](https://glass.readthedocs.io/latest/).
 
 Ideally, with the addition of every new feature to _GLASS_, documentation should
 be added using comments, docstrings, and `.rst` files.
@@ -101,12 +101,12 @@ any browser by opening the `index.html` file.
 
 ## Releases
 
-To release a new version of _GLASS_, there should be a commit titled
-`REL: glass yyyy.mm` that includes the following changes:
+To release a new version of _GLASS_, there should be a commit that includes the
+following changes:
 
-- The changelog trailers since the last release are parsed into the
-  [changelog](CHANGELOG.md) under a section titled `[yyyy.mm]  (DD Mon YYYY)`. A
-  new link to the changeset is added at the bottom of the file.
+- The changes since the last release are added to the [changelog](CHANGELOG.md)
+  under a section titled `[yyyy.mm] (DD Mon YYYY)`. A new link to the changeset
+  is added at the bottom of the file.
 - The [release notes](docs/manual/releases.rst) are updated with the new
   version. The release notes should translate the changelog entries into prose
   that can be understood by non-developer users of the code. If there are
@@ -129,14 +129,12 @@ PyPI.
 _GLASS_ follows [CalVer](https://calver.org). There is no difference between
 releases that increment the year and releases that increment the month; in
 particular, releases that increment the month may introduce breaking changes.
-The version is generate dynamically through VCS using
-[`hatch-vcs`](https://github.com/ofek/hatch-vcs).
 
-The target is to have a new _GLASS_ release at the beginning of each month, as
-long as there have been changes.
+The current version number is automatically inferred from the last release
+(i.e., git tag), subsequent unreleased commits, and local changes, if any.
 
-The current version number is automatically inferred from the last release (i.e.
-git tag), subsequent unreleased commits, and local changes, if any.
+The target is to have a new _GLASS_ release once there are significant changes
+to the code's functionality.
 
 ## Nox
 

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 <!-- Essentials -->
 
 [![PyPI](https://img.shields.io/pypi/v/glass)](https://pypi.org/project/glass)
-[![Documentation](https://readthedocs.org/projects/glass/badge/?version=latest)](https://glass.readthedocs.io/latest)
+[![Documentation](https://readthedocs.org/projects/glass/badge/?version=stable)](https://glass.readthedocs.io/stable)
 [![LICENSE](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 <!-- Code -->
@@ -80,7 +80,7 @@ e.g. a design decision or API change, you can use our [Discussions] page.
 
 We also have a public [Slack workspace] for discussions about the project.
 
-[documentation]: https://glass.readthedocs.io/
-[examples]: https://glass.readthedocs.io/projects/examples/
+[documentation]: https://glass.readthedocs.io/stable
+[examples]: https://glass.readthedocs.io/stable/examples.html
 [Discussions]: https://github.com/orgs/glass-dev/discussions
 [Slack workspace]: https://glass-dev.github.io/slack
diff --git a/docs/manual/first-steps.rst b/docs/manual/first-steps.rst
@@ -1,6 +1,4 @@
 First steps
 ===========
 
-The best way to get started with *GLASS* is to follow the examples__.
-
-__ https://glass.readthedocs.io/projects/examples/
+The best way to get started with *GLASS* is to follow the :doc:`/examples`.
diff --git a/docs/manual/releases.rst b/docs/manual/releases.rst
@@ -5,8 +5,44 @@ Release notes
 These notes document the changes between individual *GLASS* releases.
 
 
-2024.1  (16 Jul 2024)
----------------------
+2024.2 (15 Nov 2024)
+--------------------
+
+* All GLASS user functionality is now available directly from the main
+  ``glass`` namespace.  No more imports!
+
+* Changes to the functions dealing with Gaussian spectra:
+
+  * ``gaussian_gls()`` was renamed to :func:`glass.discretized_cls`, which
+    better reflects what the function does.
+
+  * The implicit call to :func:`glass.discretized_cls` was removed from
+    :func:`glass.lognormal_gls`.  Call :func:`glass.discretized_cls` explicitly
+    with the desired ``ncorr=``, ``lmax=``, and ``nside=`` parameters.
+
+* ``redshifts_from_nz()`` is deprecated in favour of :func:`glass.redshifts`,
+  as the former is almost never the right choice: the two-point statistics in a
+  linear bias model are coming from the shells, so the redshift distribution is
+  implicitly the same as the radial profile of the shells.
+
+* Several fixes to :func:`glass.ellipticity_ryden04`.
+
+* Added a FITS catalogue writer tool :func:`glass.write_catalog`.
+
+* Much improved documentation with docstring for all functions.
+
+* Examples now live in the main GLASS repository and documentation.
+
+* GLASS is now fully typed and passes mypy.
+
+* Python 3.13 is now supported.  Python 3.8 and NumPy 1.21 are no longer
+  supported.
+
+* The ``glass.core.constants`` module was removed.
+
+
+2024.1 (16 Jul 2024)
+--------------------
 
 * Further changes to the :func:`~glass.shells.partition()` function.
 

diff --git a/glass/fields.py b/glass/fields.py
@@ -62,7 +62,12 @@ def iternorm(
 
     Yields
     ------
-        The index, vector, and standard deviation for iterative sampling.
+    index
+        The index for iterative sampling.
+    vector
+        The vector for iterative sampling.
+    standard_deviation
+        The standard deviation for iterative sampling.
 
     Raises
     ------
@@ -144,6 +149,7 @@ def cls2cov(
 
     Yields
     ------
+    matrix
         The covariance matrix for iterative sampling.
 
     Raises
@@ -361,6 +367,7 @@ def generate_gaussian(
 
     Yields
     ------
+    fields
         The Gaussian random fields.
 
     Raises
@@ -450,6 +457,7 @@ def generate_lognormal(
 
     Yields
     ------
+    fields
         The lognormal random fields.
 
     """

diff --git a/glass/points.py b/glass/points.py
@@ -342,11 +342,11 @@ def uniform_positions(
 
     Yields
     ------
-    lon:
+    lon
         Columns of longitudes for the sampled points.
-    lat:
+    lat
         Columns of latitudes for the sampled points.
-    count:
+    count
         The number of sampled points. For array inputs, an array of
         counts with the same shape is returned.
 

diff --git a/glass/user.py b/glass/user.py
@@ -190,6 +190,7 @@ def write_catalog(
 
     Yields
     ------
+    writer
         The writer object.
 
     """

diff --git a/pyproject.toml b/pyproject.toml
@@ -67,7 +67,7 @@ test = [
 
 [project.urls]
 Changelog = "https://glass.readthedocs.io/stable/manual/releases.html"
-Documentation = "https://glass.readthedocs.io/"
+Documentation = "https://glass.readthedocs.io/stable"
 Homepage = "https://github.com/glass-dev/glass"
 Issues = "https://github.com/glass-dev/glass/issues"