Merge branch 'main' into ia_nla

.commitlint.rules.js

@@ -0,0 +1,13 @@
+module.exports = {
+  rules: {
+    "header-max-length": [2, "always", 65],
+    "subject-case": [0, "always", "sentence-case"],
+    "scope-enum": [2, "always", ["all", "core", "fields", "galaxies",
+                                 "lensing", "math", "observations", "points",
+                                 "shapes", "shells", "user"]],
+    "scope-case": [0, "always", "lower-case"],
+    "type-enum": [2, "always", ["API", "BUG", "DEP", "DEV", "DOC", "ENH",
+                                "MNT", "REV", "STY", "TST", "TYP", "REL"]],
+    "type-case": [0, "always", "upper-case"],
+  }
+}

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+ignore = E226,E501,E741

.github/dependabot.yml

@@ -4,3 +4,5 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    commit-message:
+      prefix: "DEV"

.github/test-constraints.txt

@@ -0,0 +1,2 @@
+--prefer-binary
+--only-binary numpy,scipy,healpy,healpix

.github/workflows/pull_request.yml

@@ -0,0 +1,28 @@
+name: Pull Request
+
+on:
+  pull_request:
+    branches:
+      - main
+    types:
+      - opened
+      - edited
+      - synchronize
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint-pr:
+    name: Formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: CondeNast/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          commitlintRulesPath: ".commitlint.rules.js"
+          commitTitleMatch: false
+          ignoreCommits: true

.github/workflows/pull_request_review.yml

@@ -0,0 +1,19 @@
+name: Pull Request Review
+
+on:
+  pull_request_review:
+    branches:
+      - main
+    types:
+      - submitted
+
+jobs:
+  approved:
+    name: Approved
+    if: github.event.review.state == 'approved'
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Add Reviewed-By
+        uses: ntessore/add-reviewed-by-action@v1

.github/workflows/release.yml

@@ -0,0 +1,20 @@
+name: Release
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  publish:
+    name: Publish on PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: publish
+      url: https://pypi.org/p/glass
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run build
+      - uses: pypa/[email protected]

.github/workflows/test.yml

@@ -0,0 +1,42 @@
+name: Test
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  style:
+    name: Style
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - run: pipx run flake8 glass
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - run: pip install -c .github/test-constraints.txt '.[test]'
+    - run: pytest --pyargs glass
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - run: pipx run build
+  docs:
+    name: Docs
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - run: pipx run --spec '.[docs]' sphinx-build -W -b html docs _build/html

.gitignore

@@ -1,7 +1,8 @@
+glass/_version.py
+
 .*.swp
 .DS_Store
 __pycache__
 docs/_build
-.tox
 build
 dist

.pre-commit-config.yaml

@@ -2,4 +2,6 @@ repos:
 - repo: https://github.com/pycqa/flake8
   rev: 4.0.1
   hooks:
-  - id: flake8
+  - id: flake8
+    additional_dependencies:
+    - flake8-print

.readthedocs.yml

@@ -1,5 +1,10 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 python:
   install:
     - method: pip

CHANGELOG.md

@@ -5,8 +5,77 @@ All notable changes to the project are documented in this file.  The format is
 based on [Keep a Changelog](https://keepachangelog.com).
 
 
-[Unreleased]
-------------
+[2023.7]  (1 Aug 2023)
+----------------------
+
+### Added
+
+* Function `getcl()` to return angular power spectra by index from
+  a list using GLASS ordering.
+* New `linear_windows()` and `cubic_windows()` window functions for
+  shells.
+
+### Changed
+
+* The `gaussian_phz()` function now accepts bounds using `lower=`
+  and `upper=` keyword parameters.
+* The `partition()` function now returns an array of weights to
+  approximate the given function by the windows.
+
+
+[2023.6]  (30 Jun 2023)
+-----------------------
+
+### Added
+
+- `deflect()` applies deflections to positions
+- `from_convergence()` returns other lensing fields given the convergence
+- A new `glass.ext` namespace, reserved for extensions
+
+### Changed
+
+- The `glass` module is no longer a namespace package
+- The point sampling functions `positions_from_delta()` and
+  `uniform_positions()` now return an iterator
+- `ellipticity_gaussian()` and `ellipticity_intnorm()` accept array inputs
+- Use pyproject.toml for packaging
+
+### Deprecated
+
+- `shear_from_convergence()` is deprecated in favour of `from_convergence()`
+
+### Removed
+
+- The `glass.all` meta-module is no longer necessary
+
+### Fixed
+
+- Incorrect extrapolation in `glass.core.array.trapz_product()`, causing a bug
+  in `glass.points.effective_bias()`
+
+
+[2023.5]  (31 May 2023)
+-----------------------
+
+### Added
+
+- Allow dimensional input to the sampling functions in `glass.points` (#80)
+- The `redshifts_from_nz()` function supports `count` arrays (#83)
+
+### Changed
+
+- Position sampling returns counts alongside points (#80)
+- `redshifts_from_nz()` no longer returns `gal_pop` (#83)
+- Move core functionality that is used by other, user-facing modules into the
+  `glass.core` module (#88)
+
+### Removed
+
+- Remove profiling functions (#89)
+
+
+[2023.2] - 1 Mar 2023
+---------------------
 
 ### Added
 
@@ -46,13 +115,16 @@ based on [Keep a Changelog](https://keepachangelog.com).
   `glass.shells` module.
 
 
-[2023.1] - 2023-01-31
----------------------
+[2023.1] - 31 Jan 2023
+----------------------
 
 ### Added
 
 - Initial wide release for GLASS paper
 
 
-[Unreleased]: https://github.com/glass-dev/glass/compare/v2023.1...HEAD
+[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
+[2023.5]: https://github.com/glass-dev/glass/compare/v2023.2...v2023.5
+[2023.2]: https://github.com/glass-dev/glass/compare/v2023.1...v2023.2
 [2023.1]: https://github.com/glass-dev/glass/releases/tag/v2023.1

CITATION.md

@@ -4,23 +4,26 @@ Citation
 If you use GLASS simulations or the GLASS library in your research, please cite
 the GLASS paper in your publications.
 
-Here is the bibliography entry from [NASA/ADS](https://ui.adsabs.harvard.edu/abs/2023arXiv230201942T):
+Here is the bibliography entry from [NASA/ADS]:
 
 ```bib
-@ARTICLE{2023arXiv230201942T,
-       author = {{Tessore}, Nicolas and {Loureiro}, Arthur and {Joachimi}, Benjamin and {von Wietersheim-Kramsta}, Maximilian},
+@ARTICLE{2023OJAp....6E..11T,
+       author = {{Tessore}, Nicolas and {Loureiro}, Arthur and {Joachimi}, Benjamin and {von Wietersheim-Kramsta}, Maximilian and {Jeffrey}, Niall},
         title = "{GLASS: Generator for Large Scale Structure}",
-      journal = {arXiv e-prints},
+      journal = {The Open Journal of Astrophysics},
      keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics},
          year = 2023,
-        month = feb,
-          eid = {arXiv:2302.01942},
-        pages = {arXiv:2302.01942},
-          doi = {10.48550/arXiv.2302.01942},
+        month = mar,
+       volume = {6},
+          eid = {11},
+        pages = {11},
+          doi = {10.21105/astro.2302.01942},
 archivePrefix = {arXiv},
        eprint = {2302.01942},
  primaryClass = {astro-ph.CO},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv230201942T},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2023OJAp....6E..11T},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 ```
+
+[NASA/ADS]: https://ui.adsabs.harvard.edu/abs/2023OJAp....6E..11T