fix a bunch of tests

.github/workflows/test_suite_nointegration.yaml

@@ -0,0 +1,113 @@
+name: Tests (No Integration 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:
+ - 'v4-prep'
+
+
+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, macos-latest]
+ python-version: [3.9, "3.10", "3.11", "3.12"]
+ 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
+ echo "extra_pytest_args=-s --log-level-21=DEBUG" >> $GITHUB_ENV
+
+ - name: Make it a Normal Run
+ if: "!contains(env.commit_message, 'ci debug')"
+ run: |
+ echo "log_level=INFO" >> $GITHUB_ENV
+ echo "extra_pytest_args=" >> $GITHUB_ENV
+
+ - name: Get C Libraries Linux
+ if: matrix.os == 'ubuntu-latest'
+ run: |
+ sudo apt-get install libfftw3-dev
+ sudo apt-get install libgsl0-dev
+
+ - name: Setup GCC
+ uses: Dup4/actions-setup-gcc@v1
+ with:
+ version: latest
+
+ - name: Install 21cmFAST Linux
+ if: matrix.os == 'ubuntu-latest'
+ run: |
+ LOG_LEVEL=${{ 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: Run Tests
+ run: |
+ python -m pytest -n 2 -l ${{ env.extra_pytest_args }} --ignore tests/test_integration_features.py --cov=py21cmfast --cov-config=.coveragerc -vv --cov-report xml:./coverage.xml --durations=25 --plots=testplots
+
+ - name: Archive Integration Test Plots
+ if: always()
+ uses: actions/upload-artifact@v3
+ with:
+ name: integration-test-plots-${{ 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')
+ with:
+ fail_ci_if_error: true
+ verbose: true
+ token: ${{ secrets.CODECOV_TOKEN }}

src/py21cmfast/outputs.py

@@ -328,7 +328,7 @@ def __init__(
  self,
  *,
  desc_redshift: float | None = None,
- buffer_size: int = 0.0,
+ buffer_size: int = 0,
  **kwargs,
  ):
  self.desc_redshift = desc_redshift

src/py21cmfast/photoncons.py

@@ -58,11 +58,11 @@
  lib.adjust_redshifts_for_photoncons()
  lib.determine_deltaz_for_photoncons() (first time only) --> calculates the deltaz array with some smoothing
  --> does more smoothing and returns the adjusted redshift
- ELIF PHOTON_CONS_TYPE==1:
+ ELIF PHOTON_CONS_TYPE==2:
  photoncons_alpha() --> computes and stores ALPHA_ESC shift vs global neutral fraction
  lib.ComputeIonizedBox()
  get_fesc_fit() --> applies the fit to the current redshift
- ELIF PHOTON_CONS_TYPE==2:
+ ELIF PHOTON_CONS_TYPE==3:
  photoncons_fesc() --> computes and stores F_ESC10 shift vs global neutral fraction
  lib.ComputeIonizedBox()
  get_fesc_fit() --> applies the fit to the current redshift
@@ -327,11 +327,13 @@ def calibrate_photon_cons(
  astro_params_photoncons = deepcopy(astro_params)
  astro_params_photoncons._R_BUBBLE_MAX = astro_params.R_BUBBLE_MAX
 
- flag_options_photoncons = FlagOptions(
- USE_MASS_DEPENDENT_ZETA=flag_options.USE_MASS_DEPENDENT_ZETA,
- M_MIN_in_Mass=flag_options.M_MIN_in_Mass,
+ flag_options_photoncons = flag_options.clone(
+ USE_TS_FLUCT=False,
+ INHOMO_RECO=False,
+ USE_MINI_HALOS=False,
+ HALO_STOCHASTICITY=False,
+ PHOTON_CONS_TYPE=0,
  )
-
  ib = None
  prev_perturb = None
 

src/py21cmfast/src/_functionprototypes_wrapper.h

@@ -9,7 +9,7 @@ int ComputePerturbField(float redshift, UserParams *user_params, CosmoParams *
 
 int ComputeHaloField(float redshift_desc, float redshift, UserParams *user_params, CosmoParams *cosmo_params,
  AstroParams *astro_params, FlagOptions *flag_options,
- InitialConditions *boxes, int random_seed, HaloField * halos_desc, HaloField *halos);
+ InitialConditions *boxes, unsigned long long int random_seed, HaloField * halos_desc, HaloField *halos);
 
 int ComputePerturbHaloField(float redshift, UserParams *user_params, CosmoParams *cosmo_params,
  AstroParams *astro_params, FlagOptions *flag_options,

tests/test_c_interpolation_tables.py

@@ -600,7 +600,7 @@ def test_SFRD_z_tables(name, plt):
  lib.init_ps()
 
  if up.INTEGRATION_METHOD_ATOMIC == 1 or up.INTEGRATION_METHOD_MINI == 1:
- lib.initialise_GL(100, np.log(M_min), np.log(M_max))
+ lib.initialise_GL(np.log(M_min), np.log(M_max))
 
  Mlim_Fstar = 1e10 * (10**ap.F_STAR10) ** (-1.0 / ap.ALPHA_STAR)
  Mlim_Fstar_MINI = 1e7 * (10**ap.F_STAR7_MINI) ** (-1.0 / ap.ALPHA_STAR_MINI)
@@ -732,7 +732,7 @@ def test_Nion_z_tables(name, plt):
  lib.init_ps()
 
  if up.INTEGRATION_METHOD_ATOMIC == 1 or up.INTEGRATION_METHOD_MINI == 1:
- lib.initialise_GL(100, np.log(M_min), np.log(M_max))
+ lib.initialise_GL(np.log(M_min), np.log(M_max))
 
  Mlim_Fstar = 1e10 * (10**ap.F_STAR10) ** (-1.0 / ap.ALPHA_STAR)
  Mlim_Fesc = 1e10 * (10**ap.F_ESC10) ** (-1.0 / ap.ALPHA_ESC)
@@ -881,7 +881,7 @@ def test_Nion_conditional_tables(name, R, mini, intmethod, plt):
  lib.init_ps()
 
  if up.INTEGRATION_METHOD_ATOMIC == 1 or up.INTEGRATION_METHOD_MINI == 1:
- lib.initialise_GL(100, np.log(M_min), np.log(M_max))
+ lib.initialise_GL(np.log(M_min), np.log(M_max))
 
  growth_out = lib.dicke(redshift)
  cond_mass = (
@@ -1067,7 +1067,7 @@ def test_SFRD_conditional_table(name, R, intmethod, plt):
  lib.init_ps()
 
  if up.INTEGRATION_METHOD_ATOMIC == 1 or up.INTEGRATION_METHOD_MINI == 1:
- lib.initialise_GL(100, np.log(M_min), np.log(M_max))
+ lib.initialise_GL(np.log(M_min), np.log(M_max))
 
  growth_out = lib.dicke(redshift)
  cond_mass = (
@@ -1230,7 +1230,7 @@ def test_conditional_integral_methods(R, name, integrand, plt):
  lib.init_ps()
 
  if up.INTEGRATION_METHOD_ATOMIC == 1 or up.INTEGRATION_METHOD_MINI == 1:
- lib.initialise_GL(100, np.log(M_min), np.log(M_max))
+ lib.initialise_GL(np.log(M_min), np.log(M_max))
 
  growth_out = lib.dicke(redshift)
  cond_mass = (

tests/test_halo_sampler.py

@@ -285,6 +285,8 @@ def test_halo_scaling_relations():
  # NOTE: Not using upper turnover, this test should be extended
  fo = FlagOptions(
  USE_MINI_HALOS=True,
+ INHOMO_RECO=True,
+ USE_TS_FLUCT=True,
  USE_HALO_FIELD=True,
  FIXED_HALO_GRIDS=False,
  HALO_STOCHASTICITY=True,

tests/test_wrapper.py

@@ -299,7 +299,11 @@ def test_run_lf():
  redshifts=[7, 8, 9],
  nbins=100,
  component=0,
- flag_options={"USE_MINI_HALOS": True},
+ flag_options={
+ "USE_MINI_HALOS": True,
+ "INHOMO_RECO": True,
+ "USE_TS_FLUCT": True,
+ },
  mturnovers=[7.0, 7.0, 7.0],
  mturnovers_mini=[5.0, 5.0, 5.0],
  )
@@ -465,7 +469,11 @@ def test_run_coeval_bad_inputs():
  ):
  wrapper.run_coeval(
  redshift=6.0,
- flag_options={"USE_MINI_HALOS": True},
+ flag_options={
+ "USE_MINI_HALOS": True,
+ "INHOMO_RECO": True,
+ "USE_TS_FLUCT": True,
+ },
  use_interp_perturb_field=True,
  )
 
@@ -588,12 +596,24 @@ def test_lc_pass_redshift_deprecation(rectlcn, ic):
 def test_coeval_lowerz_than_photon_cons(ic):
  with pytest.raises(ValueError, match="You have passed a redshift"):
  wrapper.run_coeval(
- init_box=ic, redshift=2.0, flag_options={"PHOTON_CONS_TYPE": 1}
+ init_box=ic,
+ redshift=2.0,
+ flag_options={
+ "PHOTON_CONS_TYPE": 1,
+ "USE_HALO_FIELD": False,
+ "HALO_STOCHASTICITY": False,
+ },
  )
 
 
 def test_lc_lowerz_than_photon_cons(rectlcn, ic):
  with pytest.raises(ValueError, match="You have passed a redshift"):
  wrapper.run_lightcone(
- init_box=ic, redshift=2.0, flag_options={"PHOTON_CONS_TYPE": 1}
+ init_box=ic,
+ redshift=2.0,
+ flag_options={
+ "PHOTON_CONS_TYPE": 1,
+ "USE_HALO_FIELD": False,
+ "HALO_STOCHASTICITY": False,
+ },
  )