Tests fail after #178 merged (#184)

* add setuptools_scm to tox requires

* try specify pip ver

* pip ver in workflow

* setuptools and wheel installed in workflow

* try remove pip require

* pin setuptools in workflow

* pin setuptools in workflow lower

* strip out tox-conda

* point to env yaml

* allowlist pytest

* check conda

* allowlist conda

* allowlist in correct section

* correct tox formatting

* activate env in tox

* pytest cov in reqs

* remove vestigial tox-conda comments

* fix docstrings

* update envlist

---------

Co-authored-by: Antony Lewis <[email protected]>

.github/workflows/codestyle.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Install Dependencies
         shell: bash -el {0}
         run: |
-          pip install tox-conda flake8
+          pip install tox flake8
       - name: Check Code Style
         shell: bash -el {0}
         run: |

.github/workflows/compatibility.yml

@@ -24,12 +24,14 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-activate-base: false
+          activate-environment: soliket-tests
+          environment-file: soliket-tests.yml
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
       - name: Install Dependencies
         shell: bash -el {0}
         run: |
-          pip install tox-conda
+          pip install tox
       - name: Run Tests
         shell: bash -el {0}
         run: |

.github/workflows/testing.yml

@@ -45,12 +45,14 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-activate-base: false
+          activate-environment: soliket-tests
+          environment-file: soliket-tests.yml
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
       - name: Install Dependencies
         shell: bash -el {0}
         run: |
-          pip install tox-conda
+          pip install tox
       - name: Run Tests
         shell: bash -el {0}
         run: |

pyproject.toml

@@ -13,6 +13,7 @@ dependencies = [
     "numpy",
     "scipy>=1.6",
     "pandas", # to remove
+    "pytest-cov",
     "astropy",
     "cobaya",
     "sacc",
@@ -65,7 +66,6 @@ version_file = "soliket/_version.py"
 [project.optional-dependencies]
 all = [
     "cosmopower",
-    "pyccl",
     "tensorflow_probability<0.22",
 ]
 docs = [

requirements.txt

@@ -1,6 +1,7 @@
 numpy
 scipy>=1.6
 pandas
+pytest-cov
 scikit-learn
 pyyaml
 py-bobyqa

soliket-tests.yml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   - python>=3.8,<3.12
   - pip
+  - pytest
   - pytest-cov
   - compilers
   - make

soliket/bias/bias.py

@@ -86,7 +86,7 @@ def get_Pk_gm_grid(self) -> dict:
 
 
 class Linear_bias(Bias):
-    """
+    r"""
     :Synopsis: Linear bias model.
 
     Has one free parameter, :math:`b_\mathrm{lin}` (``b_lin``).

soliket/cosmopower/cosmopower.py

@@ -220,7 +220,7 @@ def get_Cl(self, ell_factor: bool = False, units: str = "FIRASmuK2") -> dict:
         return cls
 
     def ell_factor(self, ls: np.ndarray, spectra: str) -> np.ndarray:
-        """
+        r"""
         Calculate the ell factor for a specific spectrum.
         These prefactors are used to convert from Cell to Dell and vice-versa.
 

soliket/mflike/mflike.py

@@ -115,7 +115,7 @@ def logp(self, **params_values):
         return self.loglike(cmbfg_dict)
 
     def loglike(self, cmbfg_dict):
-        """
+        r"""
         Computes the gaussian log-likelihood
 
         :param cmbfg_dict: the dictionary of theory + foregrounds
@@ -215,7 +215,7 @@ def get_cl_meta(spec):
             return exp_1, exp_2, pols, scls, symm
 
         def get_sacc_names(pol, exp_1, exp_2):
-            """
+            r"""
             Lower-level function of `prepare_data`.
             Translates the polarization combination and channel
             name of a given entry in the `spectra`
@@ -388,7 +388,7 @@ def get_sacc_names(pol, exp_1, exp_2):
         self.data = GaussianData("mflike", self.ell_vec, self.data_vec, self.cov)
 
     def _get_power_spectra(self, cmbfg):
-        """
+        r"""
         Get :math:`D_{\ell}` from the theory component
         already modified by ``theoryforge_MFLike``
 

tox.ini

@@ -1,25 +1,23 @@
 [tox]
 requires =
-	tox-conda
-	setuptools >= 30.3.0
+	setuptools >= 64
+    setuptools_scm >= 8
 	pip >= 19.3.1
 envlist =
-	py{38,39,310}-test{,-all}{,-latest,-oldest}{,-cov}
+	py{38,39,310,311}-test{,-all}{,-latest,-oldest}{,-cov}
 	codestyle
 
 [testenv]
-conda_env = soliket-tests.yml
-conda_setup_args=
-    --override-channels
-conda_install_args=
-    --override-channels
+allowlist_externals = 
+    conda
+    pytest
 
 setenv =
     COBAYA_PACKAGES_PATH = ./cobaya_packages
     SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL = True
 
 # Pass through the following environment variables which may be needed for the CI
-passenv = HOME WINDIR LC_ALL LC_CTYPE CI TRAVIS
+passenv = HOME, WINDIR, LC_ALL, LC_CTYPE, CI, TRAVIS
 
 # Run the tests in a temporary directory to make sure that we don't import
 # this package from the source tree
@@ -44,14 +42,14 @@ extras =
     all: all
 
 commands =
+    conda info
     pip freeze
     all: cobaya-install planck_2018_highl_plik.TTTEEE_lite_native --no-set-global
     !cov: pytest -vv --rootdir={toxinidir} --pyargs {toxinidir}/soliket/ {posargs}
     cov: pytest -vv --rootdir={toxinidir} --pyargs {toxinidir}/soliket/ --cov soliket --cov-report=xml --cov-config={toxinidir}/pyproject.toml {posargs}
 
 [testenv:codestyle]
 skip_install = true
-conda_env = 
 changedir = .
 description = check code style, e.g. with flake8
 deps = flake8