Merge branch 'master' into angular-lightcone

.github/workflows/test_suite.yaml

@@ -35,7 +35,13 @@ jobs:
     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@v2.1.1
         with:
@@ -55,22 +61,14 @@ jobs:
           conda config --show
           printenv | sort
 
-      - name: Logging
-        run: |
-          echo ${{ github.event.commits }}
-          echo ${{ github.event.commits[0] }}
-
       - name: Make it a Debug Run
-        if: "contains(github.event.payload.commits[0].message, 'ci debug')"
+        if: "contains(env.commit_message, 'ci debug')"
         run: |
           echo "log_level=ULTRA_DEBUG" >> $GITHUB_ENV
-          echo "extra_pytest_args='-s -k test_perturb_field_data --log-level-21=DEBUG'" >> $GITHUB_ENV
-
-      - name: 'Log Commit Message'
-        run: echo ${{ github.event.commits[0].message }}
+          echo "extra_pytest_args=-s -k "test_power_spectra_lightcone[mdz_tsfluct_nthreads]" --log-level-21=DEBUG" >> $GITHUB_ENV
 
       - name: Make it a Normal Run
-        if: "!contains(github.event.commits[0].message, 'ci debug')"
+        if: "!contains(env.commit_message, 'ci debug')"
         run: |
           echo "log_level=INFO" >> $GITHUB_ENV
           echo "extra_pytest_args=" >> $GITHUB_ENV
@@ -93,7 +91,15 @@ jobs:
 
       - name: Run Tests
         run: |
-          python -m pytest -n 2 -l --cov=py21cmfast --cov-config=.coveragerc -vv --cov-report xml:./coverage.xml --durations=25 ${{ env.extra_pytest_args }}
+          python -m pytest -n 2 -l ${{ env.extra_pytest_args }} --cov=py21cmfast --cov-config=.coveragerc -vv --cov-report xml:./coverage.xml --durations=25 --plots=testplots
+
+      - name: Archive Integration Test Plots
+        if: always() && contains(env.commit_message, 'ci debug')
+        uses: actions/upload-artifact@v3
+        with:
+          name: integration-test-plots-${{ matrix.os }}-${{ matrix.python-version }}
+          path: |
+            testplots/*.pdf
 
       - uses: codecov/codecov-action@v3
         if: matrix.os == 'ubuntu-latest' && success() && !contains(github.event.pull_request.labels.*.name, 'auto-pr')

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '(^docs/conf.py|^src/py21cmfast/_data/|changethelog.py)'
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: trailing-whitespace
           - id: check-added-large-files
@@ -17,7 +17,7 @@ repos:
           - id: mixed-line-ending
             args: ['--fix=no']
     - repo: https://github.com/pycqa/flake8
-      rev: 6.0.0  # pick a git hash / tag to point to
+      rev: 6.1.0  # pick a git hash / tag to point to
       hooks:
         - id: flake8
           additional_dependencies:
@@ -33,13 +33,13 @@ repos:
             # - flake8-copyright  # no support flor flake8 v6
             - flake8-print
 
-    - repo: https://github.com/psf/black
-      rev: 23.3.0
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 23.12.0
       hooks:
           - id: black
 
     - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
+      rev: 5.13.2
       hooks:
       - id: isort
 
@@ -51,7 +51,7 @@ repos:
       - id: rst-inline-touching-normal
 
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.7.0
+      rev: v3.15.0
       hooks:
       - id: pyupgrade
         args: [--py36-plus]

.readthedocs.yml

@@ -9,8 +9,10 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+build:
+  os: ubuntu-22.04
+  tools:
+    python: mambaforge-22.9
 
 conda:
   environment: docs/environment.yaml

CHANGELOG.rst

@@ -4,6 +4,11 @@ Changelog
 dev-version
 -----------
 
+Fixed
+~~~~~
+
+* Incorrect sign on adiabatic fluctuations.
+
 v3.3.1 [24 May 2023]
 ----------------------
 

docs/environment.yaml

@@ -5,7 +5,6 @@ channels:
 dependencies:
   - pip
   - ipython
-  - nbsphinx
   - numpydoc
   - sphinx>=1.3
   - astropy  # need this here, because we base classes off it (and docs need that).
@@ -17,3 +16,5 @@ dependencies:
     - setuptools_scm
     - bidict
     - cosmotile
+    - nbsphinx
+    - nbconvert>=6.4.5

src/py21cmfast/_utils.py

@@ -687,10 +687,6 @@ def _implementations(cls):
 
     def _init_arrays(self):
         for k, state in self._array_state.items():
-            if k == "lowres_density":
-                logger.debug("THINKING ABOUT INITING LOWRES_DENSITY")
-                logger.debug(state.initialized, state.computed_in_mem, state.on_disk)
-
             # Don't initialize C-based pointers or already-inited stuff, or stuff
             # that's computed on disk (if it's on disk, accessing the array should
             # just give the computed version, which is what we would want, not a

src/py21cmfast/src/SpinTemperatureBox.c

@@ -492,7 +492,7 @@ LOG_SUPER_DEBUG("Initialised heat");
         growthfac = growth_factor_zp * inverse_growth_factor_z;
         // read file
         #pragma omp parallel shared(this_spin_temp,xe,TK,redshift,perturbed_field, \
-                                    inverse_growth_factor_z,growth_factor_zp,cT_ad) \
+                                    growthfac,cT_ad) \
                              private(i,j,k,ct,curr_xalpha,gdens) \
                              num_threads(user_params->N_THREADS)
         {

src/py21cmfast/src/heating_helper_progs.c

@@ -316,7 +316,7 @@ double xion_RECFAST(float z, int flag)
 float cT_approx(float z)
 {
     if (global_params.USE_ADIABATIC_FLUCTUATIONS)
-        return 0.58 + 0.006*(z - 10.0);
+        return 0.58 - 0.006*(z - 10.0);
     else
         return 0.0;
 }

tests/test_integration_features.py

@@ -108,7 +108,8 @@ def test_power_spectra_lightcone(name, module_direc, plt):
             # Ensure all but 10 of the values is within 1%, and none of the values
             # is outside 10%
             assert np.all(np.abs(value - test_powers[key]) / value[0] < 1e-3)
-
+            assert np.sum(~np.isclose(value, test_powers[key], atol=0, rtol=5e-2)) < 10
+
     for key, value in true_global.items():
         print(f"Testing Global {key}")
         assert np.allclose(value, getattr(lc, key), atol=0, rtol=1e-3)