Merge branch 'master' into pr-427

Author: cmbant

.github/workflows/tests.yml

@@ -101,7 +101,7 @@ jobs:
         shell: bash -el {0}
         run: |
           pip install ruff
-          ruff check cobaya/ tests/ --output-format=github
+          ruff check cobaya/ --output-format=github
 
       - name: Install dependencies (pip)
         if: matrix.pydist != 'ANACONDA'
@@ -171,8 +171,10 @@ jobs:
     steps:
       - name: Check test results
         run: |
-          if [[ "${{ needs.tests.result }}" == "success" ]]; then
-            echo "All tests passed!"
+          result="${{ needs.tests.result }}"
+          echo "tests job result: $result"
+          if [[ "$result" == "success" || "$result" == "skipped" ]]; then
+            echo "Tests succeeded or were skipped."
             exit 0
           else
             echo "Some tests failed or were cancelled"

.gitignore

@@ -45,6 +45,7 @@ coverage.xml
 **/chains/
 my*
 scratch/
+*docker*
 
 # IDE-specific
 .idea/

CHANGELOG.md

@@ -6,6 +6,7 @@
 - Added standardized formatting with ruff (removing flake8)
 - Added pre-commit hooks for automated code quality checks (trailing whitespace, end-of-file-fixer, pyupgrade, ruff)
 - Documentation can now be built as markdown for LLM context. Flat context file provided.
+- Periodic sampled parameters implemented (for now fully supported by MCMC only), as well as tagging of derived parameters as periodic for analysis with GetDist.
 
 ### Cosmology
 

DEVEL.rst

@@ -20,11 +20,11 @@ Development flow for contributors
 
 1. Fork and clone the repo from github.
 2. From its folder, install in editable mode: ``pip install -e .``
-3. Install development dependencies: ``pip install ruff pre-commit pytest pytest-xdist pytest-cov flaky dill``
+3. Install development dependencies: ``pip install -e .[devel]``
 4. Set up pre-commit hooks: ``pre-commit install``
 5. Modify stuff.
 6. Test with pytest
-7. Make a pull requests and check (about about 15 minutes) if the tests have passed.
+7. Make a pull requests and check (about 15 minutes) if the tests have passed.
 8. Iterate until tests pass, then wait for or request feedback/merge
 
 Contributors must agree to the license (see ``LICENCE.txt`` in the root folder).

LICENCE.txt

@@ -13,24 +13,6 @@ The documentation of this program is released under the GNU Free
 Documentation License (see below)
 
 
-Exceptions:
------------
-- The copyright of the logos of the supporting institutions belong
-  to the institutions themselves
-
-
-Re-licensing of specific files:
--------------------------------
-
-The following files have been translated (some with large
-modification) and re-licensed from the more liberally licensed
-CosmoMC (https://github.com/cmbant/CosmoMC):
-
-- mcmc.py and proposal.py
-- sn.py, cmblikes.py in base_classes
-- most of the files under grid_tools/
-
-
 For this code and its documentation (with the exceptions above):
 ----------------------------------------------------------------
 

README.rst

@@ -104,3 +104,5 @@ Thanks too to `G. Cañas Herrera`_, `A. Finke`_, `X. Garrido`_, `S. Heimersheim`
    :target: https://stfc.ukri.org/
    :height: 150px
    :width: 150px
+
+(Copyright for the logos above belongs to their respective institutions.)

cobaya/collection.py

@@ -194,7 +194,7 @@ def ensure_cache_dumped(method):
 
     @functools.wraps(method)
     def wrapper(self, *args, **kwargs):
-        self._cache_dump()  # pylint: disable=protected-access
+        self._cache_dump()
         return method(self, *args, **kwargs)
 
     return wrapper
@@ -668,7 +668,6 @@ def has_int_weights(self) -> bool:
         weights = self[OutPar.weight]
         return np.allclose(np.round(weights), weights)
 
-    # pylint: disable=protected-access
     def _detempered_weights(self, with_batch=None):
         """
         Computes the detempered weights.
@@ -722,7 +721,6 @@ def _detempered_minuslogpost(self):
             -self._data[OutPar.minuslogpost].to_numpy(dtype=np.float64), self.temperature
         )
 
-    # pylint: disable=protected-access
     def reset_temperature(self, with_batch=None):
         """
         Drops the information about sampling temperature: ``weight`` and ``minuslogpost``

cobaya/component.py

@@ -329,7 +329,6 @@ def get_defaults(
         else:
             return defaults
 
-    # noinspection PyUnusedLocal
     @classmethod
     def get_modified_defaults(cls, defaults, input_options=empty_dict):
         """

cobaya/cosmo_input/autoselect_covmat.py

@@ -79,7 +79,7 @@ def get_covmat_database(installed_folders, cached=True) -> dict[CovmatFileKey, d
             log.debug("Loaded cached covmats database")
             _loaded_covmats_database[_hash] = covmat_database
             return covmat_database
-        except:
+        except Exception:
             log.info(
                 "No cached covmat database present, not usable or not up-to-date. "
                 "Will be re-created and cached."
@@ -95,7 +95,7 @@ def get_covmat_database(installed_folders, cached=True) -> dict[CovmatFileKey, d
                     header = covmat.readline()
                 assert header.strip().startswith("#")
                 params = header.strip().lstrip("#").split()
-            except:
+            except Exception:
                 continue
             name = os.path.splitext(filename)[0]
             tags = name.replace(".post.", "_").replace("_post", "").split("_")

cobaya/cosmo_input/gui.py

@@ -30,10 +30,7 @@
     font_size = "9pt"
 
 try:
-    # noinspection PyUnresolvedReferences
     from PySide6.QtCore import QPoint, QSettings, QSize, Qt, Slot
-
-    # noinspection PyUnresolvedReferences
     from PySide6.QtGui import QAction, QColor
     from PySide6.QtWidgets import (
         QAbstractItemView,
@@ -63,14 +60,11 @@ def text(key, contents):
     return desc or key
 
 
-# noinspection PyArgumentList
 def get_settings():
     return QSettings("cobaya", "gui")
 
 
-# noinspection PyArgumentList
 class MainWindow(QWidget):
-    # noinspection PyUnresolvedReferences
     def __init__(self):
         super().__init__()
         self.setWindowTitle("Cobaya input generator for Cosmology")
@@ -176,14 +170,13 @@ def __init__(self):
     def getScreen(self):
         try:
             return self.screen().availableGeometry()
-        except:
+        except Exception:
             return QApplication.screenAt(
                 self.mapToGlobal(QPoint(self.width() // 2, 0))
             ).availableGeometry()
 
     def read_settings(self):
         settings = get_settings()
-        # noinspection PyArgumentList
         screen = self.getScreen()
         h = min(screen.height() * 5 / 6.0, 900)
         size = QSize(min(screen.width() * 5 / 6.0, 1200), h)
@@ -379,13 +372,11 @@ def show_defaults(self):
         self.current_defaults_diag = DefaultsDialog(kind, component, parent=self)
 
 
-# noinspection PyUnresolvedReferences,PyArgumentList
 class DefaultsDialog(QWidget):
     def __init__(self, kind, component, parent=None):
         super().__init__()
         self.setWindowTitle(f"{kind} : {component}")
         self.setGeometry(0, 0, 500, 500)
-        # noinspection PyArgumentList
         self.move(parent.getScreen().center() - self.rect().center())
         self.show()
         # Main layout
@@ -433,7 +424,6 @@ def copy_clipb(self):
         QApplication.clipboard().setText(self.display_tabs.currentWidget().toPlainText())
 
 
-# noinspection PyArgumentList
 def gui_script():
     warn_deprecation()
     try: