Change to tox for tests

.github/workflows/testing.yml

@@ -3,66 +3,53 @@ name: Testing
 on: [push, pull_request]
 
 jobs:
-  build:
-
+  test:
+    name: ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -l {0}    
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9]
-    steps:
-    - uses: actions/checkout@v2
-
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.py }}
-        auto-update-conda: true
-        channels: conda-forge,defaults
-        channel-priority: strict
-        show-channel-urls: true
-
-    - name: install reqs
-      run: |
-        conda install pip compilers pytest pytest-cov pyccl cython
-        pip install cobaya
+        include:
 
-    - name: install extra reqs
-      run: |
-        pip install cosmopower
+          - name: latest supported versions
+            os: ubuntu-latest
+            python-version: '3.10'
+            toxenv: python3.10-test-all-latest-cov
+            toxposargs: --cov-report=xml:${GITHUB_WORKSPACE}/coverage.xml
 
-      env:  
-        MATRIX_OS: ${{ matrix.os }}
+          - name: oldest supported versions
+            os: ubuntu-latest
+            python-version: '3.7'
+            toxenv: python3.7-test-oldest
 
-    - name: Install classy
-      run: |
-        if [[ ${MATRIX_OS} == "macos-latest" ]]; then
-          . ci_scripts/install_class_osx.sh
-        else
-          . ci_scripts/install_class_linux.sh
-        fi
-        python -c "import classy; print(classy)"
-      env:
-        MATRIX_OS: ${{ matrix.os }}
+          - name: macOS 11
+            os: macos-11
+            python-version: '3.10'
+            toxenv: python3.10-test-latest
 
-    - name: install
-      run: |
-        pip install .
-
-    - name: install test data
-      run: |
-        export COBAYA_PACKAGES_PATH="../packages"
-        cobaya-install planck_2018_highl_plik.TTTEEE_lite_native
-
-    - name: Unit tests
-      run: |
-        pytest -vv soliket --cov=soliket --cov-report=xml:coverage.xml --cov-config=setup.cfg
-      env:
-        PYTEST_ADDOPTS: "--color=yes"
-
-    - name: Report Coverage (codecov)
-      if: matrix.os == 'ubuntu-latest'
-      uses: codecov/codecov-action@v2
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Install Conda w/ Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: soliket-tests
+          environment-file: soliket-tests.yml
+          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+          use-mamba: true
+          miniforge-variant: Mambaforge
+      - if: contains(matrix.os, 'ubuntu')
+        name: Install class
+        shell: bash -el {0}
+        run: |
+          pip install classy
+        env:
+          MATRIX_OS: ${{ matrix.os }}
+      - name: Run Tests
+        shell: bash -el {0}
+        run: |
+          tox -e ${{ matrix.toxenv }} ${{ matrix.toxargs }} -- ${{ matrix.toxposargs }}
+      - if: contains(matrix.toxenv, '-cov')
+        name: Report Coverage
+        uses: codecov/codecov-action@v1

ci_scripts/install_class_osx.sh

@@ -5,15 +5,20 @@ export CONDA_BUILD_SYSROOT=/
 rm -rf class_public
 git clone --depth=1000 https://github.com/lesgourg/class_public.git
 cd class_public
+git checkout v2.7.2
 
-# if you are running on macos 11.6 and higher, uncomment the following line
-sed -i.bak -e 's/gcc/gcc-9/g' Makefile
+echo "----------------------------------"
+env
+echo "----------------------------------"
 
-# if you are running on macos 10.15 and lower, uncomment the following 4 lines
-#sed -i.bak -e 's/^CC/#CC/g' Makefile
-#sed -i.bak -e 's/^OPTFLAG =/OPTFLAG = ${CFLAGS} ${LDFLAGS}/g' Makefile
-#sed -i.bak -e 's/^#CCFLAG +=/CCFLAG +=/g' Makefile
-#sed -i.bak -e 's/^#CCFLAG =/CCFLAG =/g' Makefile
+sed -i.bak -e 's/^CC/#CC/g' Makefile
+sed -i.bak -e 's/^OPTFLAG =/OPTFLAG = ${CFLAGS} ${LDFLAGS}/g' Makefile
+sed -i.bak -e 's/^#CCFLAG +=/CCFLAG +=/g' Makefile
+sed -i.bak -e 's/^#CCFLAG =/CCFLAG =/g' Makefile
+
+echo "----------------------------------"
+cat Makefile
+echo "----------------------------------"
 
 make -j4
 

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+
+requires = ["setuptools",
+            "setuptools_scm",
+            "wheel"]
+
+build-backend = 'setuptools.build_meta'

requirements.txt

@@ -0,0 +1,21 @@
+tox
+numpy
+scipy
+pandas
+scikit-learn
+pyyaml
+py-bobyqa
+packaging
+tqdm
+portalocker
+dill
+fuzzywuzzy
+astropy
+camb
+cosmopower
+getdist
+cobaya
+pyccl
+sacc
+fgspectra @ git+https://github.com/simonsobs/fgspectra@act_sz_x_cib#egg=fgspectra
+mflike @ git+https://github.com/simonsobs/lat_mflike@master

setup.cfg

@@ -1,8 +1,21 @@
-[flake8]
-select = E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,
-		 F405,F406,F5,F6,F7,F8,W1,W2,W3,W6,E501
-max-line-length = 90
-exclude = .tox,build
+[metadata]
+name = soliket
+version = 0.0
+description = "SO Likelihoods & Theories"
+
+[options]
+zip_safe = False
+packages = find:
+python_requires = >=3.7
+setup_requires = setuptools_scm
+install_requires =
+
+[options.extras_require]
+
+[options.package_data]
+soliket = *.yaml,*.bibtex,clusters/data/*,clusters/data/selFn_equD56/*,lensing/data/*.txt,mflike/*.yaml
+testpaths = "soliket"
+text_file_format = rst
 
 [coverage:run]
 omit =
@@ -27,3 +40,9 @@ exclude_lines =
     pragma: py{ignore_python_version}
     # Don't complain about IPython completion helper
     def _ipython_key_completions_
+
+[flake8]
+select = E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,
+         F405,F406,F5,F6,F7,F8,W1,W2,W3,W6,E501
+max-line-length = 90
+exclude = .tox,build

setup.py

@@ -1,36 +1,78 @@
-# example cobaya-compliant SO likelihood package;
-# adapted from github.com/cobayasampler/example_external_likelihood
+#!/usr/bin/env python
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+# NOTE: The configuration for the package, including the name, version, and
+# other information are set in the setup.cfg file.
+
+import os
+import sys
 
 from setuptools import setup
 
-setup(
-    name="soliket",
-    version="0.0",
-    description="SO Likelihoods & Theories",
-    zip_safe=False,
-    packages=["soliket", "soliket.tests", "soliket.clusters"],
-    package_data={
-        "soliket": [
-            "*.yaml",
-            "*.bibtex",
-            # "data/simulated*/*.txt",
-            "clusters/data/*",
-            "clusters/data/selFn_equD56/*",
-            "lensing/data/*.txt",
-        ]
-    },
-    install_requires=[
-        "astropy",
-        "scikit-learn",
-        "cobaya",
-        "sacc",
-        "pyccl",
-        "fgspectra @ git+https://github.com/simonsobs/fgspectra@act_sz_x_cib#egg=fgspectra", # noqa E501
-        "mflike @ git+https://github.com/simonsobs/lat_mflike@master"
-    ],
-    extras_requires=[
-        "cosmopower"
-    ],
-    test_suite="soliket.tests",
-    include_package_data=True,
-)
+
+# First provide helpful messages if contributors try and run legacy commands
+# for tests or docs.
+
+TEST_HELP = """
+Note: running tests is no longer done using 'python setup.py test'. Instead
+you will need to run:
+
+    tox -e test
+
+If you don't already have tox installed, you can install it with:
+
+    pip install tox
+
+If you only want to run part of the test suite, you can also use pytest
+directly with::
+
+    pip install -e .[test]
+    pytest
+
+For more information, see:
+
+  http://docs.astropy.org/en/latest/development/testguide.html#running-tests
+"""
+
+if 'test' in sys.argv:
+    print(TEST_HELP)
+    sys.exit(1)
+
+DOCS_HELP = """
+Note: building the documentation is no longer done using
+'python setup.py build_docs'. Instead you will need to run:
+
+    tox -e build_docs
+
+If you don't already have tox installed, you can install it with:
+
+    pip install tox
+
+You can also build the documentation with Sphinx directly using::
+
+    pip install -e .[docs]
+    cd docs
+    make html
+
+For more information, see:
+
+  http://docs.astropy.org/en/latest/install.html#builddocs
+"""
+
+if 'build_docs' in sys.argv or 'build_sphinx' in sys.argv:
+    print(DOCS_HELP)
+    sys.exit(1)
+
+VERSION_TEMPLATE = """
+# Note that we need to fall back to the hard-coded version if either
+# setuptools_scm can't be imported or setuptools_scm can't determine the
+# version, so we catch the generic 'Exception'.
+try:
+    from setuptools_scm import get_version
+    version = get_version(root='..', relative_to=__file__)
+except Exception:
+    version = '{version}'
+""".lstrip()
+
+setup(use_scm_version={'write_to': os.path.join('soliket', 'version.py'),
+                       'write_to_template': VERSION_TEMPLATE})

soliket-tests.yml

@@ -0,0 +1,16 @@
+name: soliket-tests
+channels:
+
+dependencies:
+  - python<=3.10
+  - pip
+  - compilers
+  - cmake
+  - gsl
+  - fftw
+  - cython
+  - mpi4py
+  - pytest
+  - pytest-forked
+  - pip:
+      - -r requirements.txt

soliket/tests/test_cosmopower.py

@@ -31,22 +31,26 @@
     "theory": {
         "soliket.CosmoPower": {
             # "soliket_data_path": os.path.normpath(
-            #     os.path.join(os.getcwd(), "../data/CosmoPower")
+            #     os.path.join(os.getcwd(), "soliket/data/CosmoPower")
             # ),
-            "soliket_data_path": "soliket/data/CosmoPower",
+            # "soliket_data_path": "soliket/data/CosmoPower",
             "stop_at_error": True,
         }
     },
 }
 
 
 @pytest.mark.skipif(not HAS_COSMOPOWER, reason='test requires cosmopower')
-def test_cosmopower_theory():
+def test_cosmopower_theory(request):
+    info_dict['theory']['soliket.CosmoPower']['soliket_data_path'] = \
+        os.path.join(request.config.rootdir, 'soliket/data/CosmoPower')
     model_fiducial = get_model(info_dict)   # noqa F841
 
 
 @pytest.mark.skipif(not HAS_COSMOPOWER, reason='test requires cosmopower')
-def test_cosmopower_loglike():
+def test_cosmopower_loglike(request):
+    info_dict['theory']['soliket.CosmoPower']['soliket_data_path'] = \
+        os.path.join(request.config.rootdir, 'soliket/data/CosmoPower')
     model_cp = get_model(info_dict)
 
     logL_cp = float(model_cp.loglikes({})[0])
@@ -55,7 +59,7 @@ def test_cosmopower_loglike():
 
 
 @pytest.mark.skipif(not HAS_COSMOPOWER, reason='test requires cosmopower')
-def test_cosmopower_against_camb():
+def test_cosmopower_against_camb(request):
 
     info_dict['theory'] = {'camb': {'stop_at_error': True}}
     model_camb = get_model(info_dict)
@@ -64,7 +68,8 @@ def test_cosmopower_against_camb():
 
     info_dict['theory'] = {
                            "soliket.CosmoPower": {
-                           "soliket_data_path": "soliket/data/CosmoPower",
+                           "soliket_data_path": os.path.join(request.config.rootdir,
+                                                             'soliket/data/CosmoPower'),
                            "stop_at_error": True,
                            "extra_args": {'lmax': camb_cls['ell'].max() + 1}}
         }