Merge pull request #313 from 21cmfast/angular-lightcone

Angular lightcone

.flake8

@@ -15,7 +15,7 @@ ignore =
     # Docstring in imperative mood. This should *not* be the case for @property's, but can't ignore them atm.
     D401
 max-line-length = 88
-max-complexity = 40
+max-complexity = 55
 docstring-convention=numpy
 inline-quotes="
 ignore-decorators=click.option

.github/workflows/run-tutorials.yaml

@@ -0,0 +1,111 @@
+name: Tests
+
+# Test on all pushes, except when the push is literally just a tag (because we
+# tag automatically via CI, and therefore there's no extra code in that push).
+# Also, only test on pull requests into master/production.
+on:
+  push:
+    tags-ignore:
+      - 'v*'
+  pull_request:
+    branches:
+      - 'master'
+      - 'production'
+
+
+jobs:
+  tests:
+    if: "!contains(github.event.pull_request.labels.*.name, 'auto-pr')"
+    env:
+      ENV_NAME: tests
+      PYTHON: ${{ matrix.python-version }}
+      OS: ${{ matrix.os }}
+      CC: gcc
+    name: Testing
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+        tutorial: ["coeval_cubes", "gather_data", "lightcones"]
+    defaults:
+     run:
+       # Adding -l {0} ensures conda can be found properly in each step
+       shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@master
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          fetch-depth: 0
+
+      - name: Print head git commit message
+        id: get_head_commit_message
+        run: echo "commit_message=$(git show -s --format=%s)" >> "$GITHUB_ENV"
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          # auto-update-conda: true
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/${{ matrix.os }}-env.yml
+          activate-environment: tests
+          channel-priority: true
+
+      - name: Conda Info
+        run: |
+          conda info -a
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Make it a Debug Run
+        if: "contains(env.commit_message, 'ci debug')"
+        run: |
+          echo "log_level=ULTRA_DEBUG" >> $GITHUB_ENV
+
+      - name: Make it a Normal Run
+        if: "!contains(env.commit_message, 'ci debug')"
+        run: |
+          echo "log_level=INFO" >> $GITHUB_ENV
+
+      - name: Get C Libraries Linux
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get install libfftw3-dev
+          sudo apt-get install libgsl0-dev
+
+      - name: Setup GCC
+        uses: Dup4/actions-setup-gcc@v1
+        with:
+          version: latest
+
+      - name: Install 21cmFAST Linux
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          LOG_LEVEL=${{ env.log_level }} pip install .
+
+      - name: Install 21cmFAST MacOS
+        if: matrix.os == 'macos-latest'
+        run: |
+          LOG_LEVEL=${{ env.log_level }} CFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" pip install .
+
+      - name: Setup papermill
+        run: |
+          pip install papermill
+          pip install ipykernel
+          python -m ipykernel install --user --name=tests
+
+      - name: Run
+        run: |
+            TEST_RUN=True papermill -k tests --request-save-on-cell-execute docs/tutorials/${{ matrix.tutorial }}.ipynb ${{ matrix.tutorial }}.ipynb
+
+      - name: Archive Notebooks
+        uses: actions/upload-artifact@v3
+        with:
+          name: tutorials-${{ matrix.tutorial }}
+          path: |
+            ${{ matrix.tutorial }}.ipynb

.github/workflows/test_suite.yaml

@@ -27,7 +27,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.9, "3.10", "3.11"]
     defaults:
      run:
        # Adding -l {0} ensures conda can be found properly in each step
@@ -43,15 +43,15 @@ jobs:
         run: echo "commit_message=$(git show -s --format=%s)" >> "$GITHUB_ENV"
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.1.1
+        uses: conda-incubator/setup-miniconda@v3
         with:
           # auto-update-conda: true
-          miniconda-version: "latest"
+          mamba-version: "*"
+          channels: conda-forge,defaults
           python-version: ${{ matrix.python-version }}
           environment-file: ci/${{ matrix.os }}-env.yml
           activate-environment: tests
-          channel-priority: strict
-          use-only-tar-bz2: true
+          channel-priority: true
 
       - name: Conda Info
         run: |
@@ -79,6 +79,11 @@ jobs:
           sudo apt-get install libfftw3-dev
           sudo apt-get install libgsl0-dev
 
+      - name: Setup GCC
+        uses: Dup4/actions-setup-gcc@v1
+        with:
+          version: latest
+
       - name: Install 21cmFAST Linux
         if: matrix.os == 'ubuntu-latest'
         run: |

CHANGELOG.rst

@@ -4,6 +4,42 @@ Changelog
 dev-version
 -----------
 
+Deprecations
+~~~~~~~~~~~~
+
+* Python <3.9 is no longer supported.
+
+Fixed
+~~~~~
+
+* Fixed small issue in ``Lightcone.lightcone_coords``.
+
+Added
+~~~~~
+
+* New ``Lightconer`` base class with user-facing classes ``RectilinearLightconer`` and
+  ``AngularLightconer``. These are now the recommended way to define how lightcones
+  should be created. Note that these are *not* the final lightcone object, but simply a
+  "definition" for how to create the lightcone.
+* The ``Lightcone`` class still exists, but is now joined by an ``AngularLightcone``
+  class that is the output lightcone when using the ``AngularLightconer`` definition.
+* New ``KEEP_3D_VELOCITIES`` user-param. This is *required* to be True if you want to
+  apply RSDs to an ``AngularLightcone``.
+* Ability to check-point lightcone creation, so that it can be resumed later. Simply
+  pass the ``lightcone_fname`` argument to ``run_lightcone``.
+* New ``cache_tools.get_boxes_at_redshift`` function to get all boxes at a given
+  redshift, regardless of the parameters used to create them.
+* New ``CosmoParams.from_astropy()`` classmethod for constructing a cosmo params object
+  directly from an astropy cosmology.
+
+
+Internals
+~~~~~~~~~
+
+* Refactored RSDs to the ``subcell_rsds.c`` C-module.
+* Added CI testing of the docs tutorials.
+* More precise debugging summaries of boxes in the C code.
+
 Fixed
 ~~~~~
 

ci/macos-latest-env.yml

@@ -17,7 +17,7 @@ dependencies:
   - pip
   - gsl
   - fftw
-  - conda-forge/label/cf201901::gcc
+  #- gcc
   - pip:
     - powerbox
     - cached_property

docs/conf.py

@@ -25,10 +25,6 @@ def __getattr__(cls, name):
     "click",
     "tqdm",
     "pyyaml",
-    "scipy",
-    "scipy.interpolate",
-    "scipy.integrate",
-    "scipy.special",
     "h5py",
     "cached_property",
 ]

docs/environment.yaml

@@ -15,5 +15,7 @@ dependencies:
     - sphinx-rtd-theme
     - setuptools_scm
     - bidict
+    - cosmotile
     - nbsphinx
     - nbconvert>=6.4.5
+    - cffi