Merge branch 'master' into profile_sampler

.github/workflows/tests.yml

@@ -0,0 +1,116 @@
+name: CI
+
+# for the moment only runs on "action* branches". Coverage/pypi not yet set up.
+
+on:
+  push:
+    branches:
+      - 'action*'
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+env:
+  COBAYA_INSTALL_SKIP: polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck,classy
+  COBAYA_PACKAGES_PATH: ../packages
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: "Anaconda: jammy LTS Python (fast; pip CAMB)"
+            os: ubuntu-latest
+            pydist: "ANACONDA"
+          - name: "Latest Python 3.12"
+            os: ubuntu-latest
+            python-version: 3.12
+            mpi: openmpi
+          - name: "OS X Python 3.8"
+            os: macos-latest
+            python-version: 3.8
+            mpi: openmpi
+          - name: "Windows Python 3.12"
+            os: windows-latest
+            python-version: 3.12
+            mpi: intelmpi
+    steps:
+    - run: ln -s $(which gfortran-14) /usr/local/bin/gfortran
+      if: matrix.os == 'macos-latest'
+
+    - run: gfortran --version
+
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python ${{ matrix.python-version }}
+      if: matrix.pydist != 'ANACONDA'
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up Miniconda
+      if: matrix.pydist == 'ANACONDA'
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-activate-base: false
+        activate-environment: tests-environment
+        environment-file: tests-environment.yml
+
+    - name: Install mpi
+      if: matrix.pydist != 'ANACONDA'
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: ${{ matrix.mpi }}
+
+#    - name: Cache dependencies
+#      uses: actions/cache@v2
+#      with:
+#        path: |
+#          ${{ github.workspace }}/packages/data/planck_supp_data_and_covmats
+#          ${{ github.workspace }}/packages/data/bao_data
+#          ${{ github.workspace }}/packages/data/sn_data
+#          ${{ github.workspace }}/packages/data/des_data
+#          ${{ github.workspace }}/packages/data/planck_2018_pliklite_native
+#        key: ${{ runner.os }}-build-${{ matrix.python-version }}}
+
+    - name: Install dependencies (pip)
+      if: matrix.pydist != 'ANACONDA'
+      run: |
+        pip install mpi4py -i https://pypi.anaconda.org/mpi4py/simple
+        pip install -r requirements.txt pytest-xdist pytest-cov flaky matplotlib dill coverage flake8 iminuit numba camb
+
+    - name: Run flake8
+      shell: bash -el {0}
+      run: |
+        flake8 cobaya --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 --show-source --statistics
+
+    - name: Run cobaya install and tests
+      shell: bash -el {0}
+      run: |
+        coverage run --parallel-mode -m cobaya.install polychord --debug
+        coverage run --parallel-mode -m pytest tests/ -n auto -k "not cosmo" --skip-not-installed --no-flaky-report
+        coverage run --parallel-mode -m cobaya.install cosmo-tests --no-progress-bars --debug --skip-global
+        pytest tests/ --cov -vv -s -k "cosmo" -n 2 --skip-not-installed --no-flaky-report
+
+    - name: Run MPI tests
+      shell: bash -el {0}
+      run: |
+        mpiexec -np 2 coverage run --parallel-mode -m pytest -x -m mpi tests/ --no-flaky-report
+
+    - name: Run external likelihood tests
+      shell: bash -el {0}
+      run: |
+        git clone --depth=1 https://github.com/CobayaSampler/example_external_likelihood
+        pip install ./example_external_likelihood --quiet
+        coverage run --parallel-mode -m unittest test_package.tests.test
+
+#    - name: Upload coverage to Codecov
+#      uses: codecov/codecov-action@v1
+
+

.travis.yml

@@ -8,7 +8,7 @@ env:
   global:
     - COBAYA_INSTALL_SKIP=polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck
 
-if: (type = pull_request) OR (branch = master) OR (branch =~ ^test.*) OR (tag IS present)
+if: (type = pull_request) OR (branch = master) OR (branch =~ ^test.*) OR (branch =~ ^alltest.*) OR (tag IS present)
 
 #Large CamSpec folders tend to hang, so exclude non-base likelihoods from cache
 cache:
@@ -21,8 +21,6 @@ cache:
     - /home/travis/build/CosmoPars/packages/data/sn_data
     - /home/travis/build/CosmoPars/packages/data/des_data
     - /home/travis/build/CosmoPars/packages/data/planck_2018_pliklite_native
-    - /home/travis/build/CosmoPars/packages/data/planck_2018_lowE_native
-    - /home/travis/build/CosmoPars/packages/data/planck_2018_lowT_native
 
 # (Pre)Installation
 jobs:
@@ -46,29 +44,29 @@ jobs:
         apt:
           packages:
             - gfortran
+      install:
+        - pip install -r requirements.txt camb
       env:
         - GCC_VERSION="ubuntu"
       python: "3.10"
-    - if: branch !~ ^test.*
-      name: "Anaconda: jammy LTS Python 3.11"
+    - name: "Anaconda: jammy LTS Python (fast; pip CAMB)"
       dist: jammy
-      addons:
-        apt:
-          packages:
-            - gfortran
       env:
         - GCC_VERSION="ubuntu"
         - PYDIST="ANACONDA"
         - ANACONDA_CHANNEL="defaults"
-      python: "3.11"
-    - name: "Latest jammy Python 3.12"
+        - COBAYA_INSTALL_SKIP="$COBAYA_INSTALL_SKIP,classy"
+      language: minimal
+    - if: branch !~ ^test.*
+      name: "Latest jammy Python 3.12"
       dist: jammy
       addons:
         apt:
           packages:
             - gfortran
       env:
         - GCC_VERSION="ubuntu"
+        - COBAYA_INSTALL_SKIP="$COBAYA_INSTALL_SKIP,classy"
       python: "3.12"
 
 
@@ -81,27 +79,25 @@ before_install:
     ln -s /usr/bin/g++-$GCC_VERSION gcc-symlinks/g++;
     export PATH=$PWD/gcc-symlinks:$PATH;
     fi
-  - if [[ "$GCC_VERSION" == "11" ]]; then
-    export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgfortran.so.5;
-    fi
-  - gfortran --version
+  - which gfortran >/dev/null 2>&1 && gfortran --version || echo "gfortran not installed"
   # Install rest of system requisites
-  - sudo apt install openmpi-bin openmpi-common libopenmpi-dev libopenblas-dev liblapack-dev
+  # - sudo apt install openmpi-bin openmpi-common libopenmpi-dev libopenblas-dev liblapack-dev
   # Python requisites
   - if [[ "$PYDIST" == "ANACONDA" ]]; then
-    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
     bash miniconda.sh -b -p $HOME/miniconda;
     export PATH="$HOME/miniconda/bin:$PATH";
     hash -r;
     conda config --set always_yes yes --set changeps1 no;
     conda info -a;
-    conda create -q -n test-environment -c $ANACONDA_CHANNEL python=$TRAVIS_PYTHON_VERSION scipy matplotlib cython PyYAML dill coverage pytest;
+    conda create -q -n test-environment -c $ANACONDA_CHANNEL scipy matplotlib cython PyYAML dill coverage pytest pandas;
     source activate test-environment;
     conda install -c conda-forge mpi4py openmpi iminuit;
-    pip install flake8 flaky pytest-forked pytest-cov;
+    pip install -r requirements.txt flake8 flaky pytest-xdist pytest-cov camb;
     else
     python -m pip install --upgrade pip setuptools wheel;
-    pip install mpi4py "numpy<2" pytest-forked pytest-cov flaky matplotlib dill coverage flake8 iminuit;
+    pip install openmpi mpi4py -i https://pypi.anaconda.org/mpi4py/simple;
+    pip install pytest-xdist pytest-cov flaky matplotlib dill coverage flake8 iminuit numba;
     fi
   - python --version
 
@@ -112,11 +108,9 @@ script:
   # General tests:
   - export COBAYA_PACKAGES_PATH="../packages"
   - coverage run --parallel-mode -m cobaya.install polychord --debug
-  - coverage run --parallel-mode -m pytest tests/ -k "not cosmo" --skip-not-installed --no-flaky-report
-  # numba can speed things, but makes for some messy logs
-  # - pip install numba
+  - coverage run --parallel-mode -m pytest tests/ -n auto -k "not cosmo" --skip-not-installed --no-flaky-report
   # Cosmology tests:
-  - coverage run --parallel-mode -m cobaya.install cosmo-tests --no-progress-bars --debug
+  - coverage run --parallel-mode -m cobaya.install cosmo-tests --no-progress-bars --debug --skip-global
   - if [ -n "${CAMB_BRANCH}" ]; then
     rm -rf $COBAYA_PACKAGES_PATH/code/CAMB ;
     git clone --recursive --depth 1 -b $CAMB_BRANCH https://github.com/cmbant/CAMB $COBAYA_PACKAGES_PATH/code/CAMB ;
@@ -125,10 +119,10 @@ script:
   # mpi tests
   - mpiexec -np 2 --mca orte_base_help_aggregate 0 --mca btl ^openib --oversubscribe coverage run --parallel-mode -m pytest -x -m mpi tests/ --no-flaky-report ;
   - mkdir covers; mv .coverage.* covers; ls -ltra covers
-  - pytest tests/ --cov -vv -s -k "cosmo" --forked --skip-not-installed --no-flaky-report
+  - pytest tests/ --cov -vv -s -k "cosmo" -n 1 --skip-not-installed --no-flaky-report
   - mv .coverage .coverage.pytest; mv covers/.cov* .
   # Test external cosmological likelihoods
-  - pip install -e $COBAYA_PACKAGES_PATH/code/CAMB --quiet
+  #- pip install -e $COBAYA_PACKAGES_PATH/code/CAMB --quiet
   #- git clone --depth=1 https://github.com/CobayaSampler/planck_lensing_external
   #- pip install ./planck_lensing_external --quiet
   #- coverage run --parallel-mode -m unittest plancklensing.tests.test_likes

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 3.5.x
+
+- Detect and fix incomplete last lines when resuming or minimizing from existing runs (#306, #378)
+- Added functions module and refactored some numerical functions into it
+
 ## 3.5.4
 
 - Allow classes to have both yaml and class attributes as long as no duplicate keys

DEVEL.rst

@@ -21,7 +21,7 @@ Development flow for contributors
 1. Fork and clone the repo from github.
 2. From its folder, install in editable mode: ``pip install -e .``
 3. Modify stuff.
-4. Test with pytest (first "pip install pytest pytest-forked pytest-cov flaky dill")
+4. Test with pytest (first "pip install pytest pytest-xdist pytest-cov flaky dill")
 5. Make a pull requests and check (about about 15 minutes) if the tests have passed.
 6. Iterate until tests pass, then wait for or request feedback/merge
 

TODO.md

@@ -5,7 +5,7 @@
 # cosmetic/consistency/speed
 
 ## min/max bounds enforced on derived parameters (more generally, "bounds" as well as priors)
-## make portalocker/numba/dill a requirement?
+## make numba a requirement?
 ## version attribute should be in all components not just theory (samplers can have versions) [done for samplers; missing: likelihoods]
 ## In the docs "Bases" (and UML diagram) not hyperlinked correctly (not sure how to fix)
 ## dump log info along with each chain file if saving to file (currently in stdout)

cobaya/__main__.py

@@ -13,7 +13,7 @@ def run_command():
     prefix = "cobaya-"
     console_scripts = (
         metadata.entry_points().select(group="console_scripts")
-        if sys.version_info > (3, 9)
+        if sys.version_info >= (3, 10)
         else metadata.entry_points()["console_scripts"]
     )
     for script in console_scripts:

cobaya/collection.py

@@ -96,7 +96,7 @@ def compute_temperature(logpost, logprior, loglike, check=True, extra_tolerance=
     """
     Returns the temperature of a sample.
 
-    If ``check=True`` and the log-probabilites passed are arrays, checks consistency
+    If ``check=True`` and the log-probabilities passed are arrays, checks consistency
     of the sample temperature, and raises ``AssertionError`` if inconsistent.
     """
     temp = (logprior + loglike) / logpost
@@ -286,8 +286,7 @@ def __init__(self, model, output=None, cache_size=_default_cache_size, name=None
             self.reset()
         # If loaded, check sample weights, consistent logp sums,
         # and temperature (ignores the given one)
-        samples_loaded = len(self) > 0
-        if samples_loaded:
+        if len(self) > 0:
             try:
                 try:
                     self.temperature = self._check_logps(extra_tolerance=False)
@@ -499,8 +498,9 @@ def _check_logps(self, temperature_only=False, extra_tolerance=False):
                 check=True, extra_tolerance=extra_tolerance)
         except AssertionError as excpt:
             raise LoggedError(
-                self.log, "The sample seems to have an inconsistent temperature.") \
-                from excpt
+                self.log, "The sample seems to have an inconsistent temperature.  "
+                          "This could be due to input file truncation on the last line "
+                          "due to crash/being killed before complete.") from excpt
         if not temperature_only:
             tols = {
                 "rtol": 1e-4 * (10 if extra_tolerance else 1),

cobaya/component.py

@@ -444,9 +444,7 @@ def compare_versions(cls, version_a, version_b, equal=True):
         :return: bool
         """
         va, vb = version.parse(version_a), version.parse(version_b)
-        if va >= vb if equal else va > vb:
-            return True
-        return False
+        return va >= vb if equal else va > vb
 
     def __exit__(self, exception_type, exception_value, traceback):
         if self.timer and self.timer.n:
@@ -482,6 +480,7 @@ def dump_timing(self):
     def get_versions(self, add_version_field=False) -> InfoDict:
         """
         Get version dictionary
+
         :return: dictionary of versions for all components
         """
 
@@ -494,6 +493,7 @@ def format_version(x):
     def get_speeds(self, ignore_sub=False) -> InfoDict:
         """
         Get speeds dictionary
+
         :return: dictionary of versions for all components
         """
         from cobaya.theory import HelperTheory
@@ -695,8 +695,7 @@ def module_class_for_name(m, name):
     for cls in classes_in_module(m, subclass_of=CobayaComponent):
         if cls.__name__.lower() in valid_names:
             if result is not None:
-                raise ValueError('More than one class with same lowercase name %s',
-                                 name)
+                raise ValueError(f'More than one class with same lowercase name {name}')
             result = cls
     return result
 
@@ -777,7 +776,7 @@ def _bare_load_external_module(name, path=None, min_version=None, reload=False,
 
 def load_external_module(module_name=None, path=None, install_path=None, min_version=None,
                          get_import_path=None, reload=False, logger=None,
-                         not_installed_level=None):
+                         not_installed_level=None, default_global=False):
     """
     Tries to load an external module at initialisation, dealing with explicit paths
     and Cobaya's installation path.
@@ -807,12 +806,14 @@ def load_external_module(module_name=None, path=None, install_path=None, min_ver
     found. If this exception will be handled at a higher level, you may pass
     `not_installed_level='debug'` to prevent printing non-important messages at
     error-level logging.
+
+    If default_global=True, always attempts to load from the global path if not
+    installed at path (e.g. pip install).
     """
     if not logger:
         logger = get_logger(__name__)
     load_kwargs = {"name": module_name, "path": path, "get_import_path": get_import_path,
                    "min_version": min_version, "reload": reload, "logger": logger}
-    default_global = False
     if isinstance(path, str):
         if path.lower() == "global":
             msg_tried = "global import (`path='global'` given)"

cobaya/containers.py

@@ -47,7 +47,7 @@
 # Python requisites -- LC_ALL=C: Necessary just for pip <= 8.1.2 (Xenial version)
 ENV LC_ALL C
 RUN python -m pip install --upgrade pip
-RUN python -m pip install pytest-forked matplotlib cython astropy --upgrade
+RUN python -m pip install pytest-xdist matplotlib cython astropy --upgrade
 # Prepare environment and tree for external packages -------------------------
 ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/usr/local/lib
 ENV CONTAINED TRUE

cobaya/cosmo_input/autoselect_covmat.py

@@ -205,7 +205,7 @@ def score_likes(_key: CovmatFileKey, covmat):
     best_p_l = get_best_score(best_p, score_likes)
     if is_debug(log):
         log.debug("Subset based on params + likes:\n - " +
-                  "\n - ".join([b["name"] for b in best_p_l]))
+                  "\n - ".join([b["name"] for b in best_p_l.values()]))
 
     if key_tuple:
         def score_left_params(_key, _covmat):