Merge branch 'develop' of https://github.com/AequilibraE/aequilibrae …

…into renata/528-add-support-to-more-than-one-transit-agency-in-gtfs-feeds

.github/workflows/build_wheels.yml

@@ -1,8 +1,34 @@
 name: Build
 
-on: [pull_request]
+on:
+ push:
+    branches:
+      - 'develop'
+ pull_request:
+ release:
+     types: [published]
+
 
 jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+#      - name: Test if SDist build has all necessary pieces to be installed
+#        run: |
+#          pip3 install setuptools build --upgrade
+#          pip3 install dist/*.tar.gz
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -27,20 +53,6 @@ jobs:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
-  make_sdist:
-    name: Make SDist
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Build SDist
-        run: pipx run build --sdist
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: cibw-sdist
-          path: dist/*.tar.gz
-
   upload_all:
     needs: [build_wheels, make_sdist]
     environment: pypi
@@ -55,4 +67,4 @@ jobs:
         path: dist
         merge-multiple: true
 
-    - uses: pypa/gh-action-pypi-publish@release/v1
+    - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/documentation.yml

@@ -6,6 +6,8 @@ on:
      - develop
  pull_request:
  release:
+     types: [published]
+
 
 jobs:
   build:
@@ -44,30 +46,18 @@ jobs:
     - name: Test docstrings
       run: |
         python -m pytest --doctest-modules aequilibrae/log.py aequilibrae/parameters.py aequilibrae/paths/vdf.py
+        python -m pytest docs/source/modeling_with_aequilibrae/project_pieces --doctest-glob=*.rst
 
     - name: Build documentation
       run: |
-        jupyter nbconvert --to rst docs/source/validation_benchmarking/IPF_benchmark.ipynb
+        jupyter nbconvert --to rst docs/source/useful_information/validation_benchmarking/IPF_benchmark.ipynb
         sphinx-build -M latexpdf docs/source docs/source/_static
         sphinx-build -b html docs/source docs/build
         python3 -m zipfile -c AequilibraE.zip docs/build
         cp AequilibraE.zip docs/source/_static
         cd docs
         make html
 
-    - name: Upload to DEV on S3
-      if: ${{ (github.event_name == 'pull_request') && (env.HAS_SECRETS == 'true') }}
-      uses: jakejarvis/s3-sync-action@master
-      with:
-        args: --acl public-read --follow-symlinks --delete
-      env:
-        AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-        AWS_REGION: 'us-east-1'   # optional: defaults to us-east-1
-        SOURCE_DIR: 'docs/build/html/'      # optional: defaults to entire repository
-        DEST_DIR: 'python/dev/'      # optional: defaults to entire repository
-
     - name: Upload to develop branch to S3
       if: ${{ (github.ref == 'refs/heads/develop') && (github.event_name == 'push') && (env.HAS_SECRETS == 'true') }}
       uses: jakejarvis/s3-sync-action@master
@@ -123,3 +113,20 @@ jobs:
         AWS_REGION: 'us-east-1'   # optional: defaults to us-east-1
         SOURCE_DIR: 'docs/build/htmlv/'      # optional: defaults to entire repository
         DEST_DIR: 'python/'      # optional: defaults to entire repository
+
+    - name: Rename documentation folder to push to S3 DEV
+      if: ${{ (github.event_name == 'pull_request') && (env.HAS_SECRETS == 'true') }}
+      run: mv docs/build/html/ docs/build/${{ github.event.number }}/
+
+    - name: Upload to DEV on S3
+      if: ${{ (github.event_name == 'pull_request') && (env.HAS_SECRETS == 'true') }}
+      uses: jakejarvis/s3-sync-action@master
+      with:
+        args: --acl public-read --follow-symlinks --delete
+      env:
+        AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        AWS_REGION: 'us-east-1'   # optional: defaults to us-east-1
+        SOURCE_DIR: 'docs/build/'      # optional: defaults to entire repository
+        DEST_DIR: 'python/dev/'      # optional: defaults to entire repository

.gitignore

@@ -2,6 +2,11 @@
 _build
 _static
 _templates
+docs/source/sg_execution_times.rst
+docs/source/_auto_examples
+docs/source/api/generated
+docs/source/modeling_with_aequilibrae/project_database/data_model
+docs/source/modeling_with_aequilibrae/transit_database/data_model
 
 # User-specific stuff:
 .idea/**/workspace.xml

aequilibrae/matrix/aequilibrae_matrix.py

@@ -93,6 +93,8 @@ def save(self, names=(), file_name=None) -> None:
 
         :Arguments:
             **names** (:obj:`tuple(str)`, *Optional*): New names for the matrices. Required if working with OMX files
+
+            **file_name** (:obj:`str`, *Optional*): Local path to the matrix file
         """
         if file_name is not None:
             cores = names if len(names) else self.names
@@ -293,21 +295,22 @@ def create_from_omx(
         Creates an AequilibraeMatrix from an original OpenMatrix
 
         :Arguments:
-            **file_path** (:obj:`str`): Path for the output AequilibraEMatrix
+            **file_path** (:obj:`str`): Path for the output AequilibraeMatrix
 
             **omx_path** (:obj:`str`): Path to the OMX file one wants to import
 
-            **cores** (:obj:`list`): List of matrix cores to be imported
+            **cores** (:obj:`list`, *Optional*): List of matrix cores to be imported
 
-            **mappings** (:obj:`list`): List of the matrix mappings (i.e. indices, centroid numbers) to be imported
+            **mappings** (:obj:`list`, *Optional*): List of the matrix mappings (i.e. indices, centroid numbers)
+            to be imported
 
-            **robust** (:obj:`bool`, *Optional*): Boolean for whether AequilibraE should try to adjust the names for cores
-            and indices in case they are too long. Defaults to True
+            **robust** (:obj:`bool`, *Optional*): Boolean for whether AequilibraE should try to adjust the names
+            for cores and indices in case they are too long. Defaults to ``True``
 
             **compressed** (:obj:`bool`, *Optional*): Boolean for whether we should compress the output matrix.
             Not yet implemented
 
-            **memory_only** (:obj:`bool`, *Optional*): Whether you want to keep the matrix copy in memory only. Defaults to True
+            **memory_only** (:obj:`bool`, *Optional*): Whether you want to keep the matrix copy in memory only. Defaults to ``True``
 
         """
 
@@ -405,7 +408,7 @@ def create_from_trip_list(self, path_to_file: str, from_column: str, to_column:
 
             **from_column** (:obj:`str`): trip list file column containing the origin zones numbers
 
-            **from_column** (:obj:`str`): trip list file column containing the destination zones numbers
+            **to_column** (:obj:`str`): trip list file column containing the destination zones numbers
 
             **list_cores** (:obj:`list`): list of core columns in the trip list file
 
@@ -840,7 +843,7 @@ def load(self, file_path: str):
             self.__load_aem__()
 
     def is_omx(self):
-        """Returns ``True`` if matrix data source is OMX, False otherwise"""
+        """Returns ``True`` if matrix data source is OMX, ``False`` otherwise"""
         return self.__omx
 
     def computational_view(self, core_list: List[str] = None):
@@ -920,7 +923,7 @@ def copy(
             **output_name** (:obj:`str`): Name of the new matrix file.
             If none is provided, returns a copy in memory only
 
-            **cores** (:obj:`list`):List of the matrix cores to be copied
+            **cores** (:obj:`list`): List of the matrix cores to be copied
 
             **names** (:obj:`list`, *Optional*): List with the new names for the cores. Defaults to current names
 
@@ -1044,7 +1047,7 @@ def columns(self) -> np.ndarray:
 
     def nan_to_num(self):
         """
-        Converts all NaN values in all cores in the computational view to zeros
+        Converts all ``NaN`` values in all cores in the computational view to zeros
 
         .. code-block:: python
 

aequilibrae/matrix/coo_demand.pyx

@@ -66,7 +66,7 @@ cdef class GeneralisedCOODemand:
             dfs.append(df.dropna())
 
         self.add_df(dfs, shape=shape, fill=fill)
-        logging.info(f"There {len(self.df):,} are OD pairs with non-zero flows")
+        logging.info(f"There are {len(self.df):,} OD pairs with non-zero flows")
 
     def _initalise_col_names(self):
         """

aequilibrae/parameters.py

@@ -6,16 +6,24 @@
 
 
 class Parameters:
-    """Global parameters module
+    """Global parameters module.
+
+    Parameters are used in many procedures, and are often defined in the ``parameters.yml`` file ONLY.
 
-    Parameters are used in many procedures, and are often defined only in the parameters.yml file ONLY
     Parameters are organized in the following groups:
 
     * assignment
     * distribution
+    * network
+      * links
+      * modes
+      * nodes
+      * osm
+      * gmns
+    * osm
     * system
-    * report zeros
-    * temp directory
+
+    Please observe that OSM information handled on network is not the same on the OSM group.
 
     .. code-block:: python