diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index c0da4f0156dc2af48a4ba80b4d0af69c62cd5c3e..588476bd624f7e24a5e0f49380fb1e66f5bd1b17 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -27,12 +27,14 @@
CaosDB can automatically be filled with Records based on some structure, a file
structure, a table or similar.
+
The Crawler will iterate over the respective items and test for each item
whether a CFood class exists that matches the file path, i.e. whether CFood
class wants to treat that pariticular item. If one does, it is instanciated to
treat the match. This occurs in basically three steps:
+
1. Create a list of identifiables, i.e. unique representation of CaosDB Records
-(such as an experiment belonging to a project and a date/time).
+ (such as an experiment belonging to a project and a date/time).
2. The identifiables are either found in CaosDB or they are created.
3. The identifiables are update based on the date in the file structure.
"""
@@ -333,7 +335,7 @@ class AbstractFileCFood(AbstractCFood):
out : str
The regular expression, starting with ``.*\\.`` and ending with the EOL dollar
character. The actual extension will be accessible in the
- :py:attribute:`pattern group name<python:re.Pattern.groupindexe>` ``ext``.
+ :py:attr:`pattern group name <python:re.Pattern.groupindex>` ``ext``.
"""
if not extensions:
diff --git a/src/caosadvancedtools/cfoods/h5.py b/src/caosadvancedtools/cfoods/h5.py
index f3d41dd0037ce9393b5b7dac3cc5bb6cc3db41d8..dfd6f2905c955c1b4e493da1f2cbf45583ee68dc 100644
--- a/src/caosadvancedtools/cfoods/h5.py
+++ b/src/caosadvancedtools/cfoods/h5.py
@@ -22,8 +22,7 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
-"""A CFood for hdf5 files
-
+"""A CFood for hdf5 files.
This module allows to parse hdf5 files and reproduce their structure in form
of Records that reference each other.
@@ -130,7 +129,7 @@ class H5CFood(AbstractFileCFood):
@staticmethod
def get_re():
- """Return a regular expression string to match *.h5, *.nc, *.hdf, *.hdf5."""
+ """Return a regular expression string to match ``*.h5``, ``*.nc``, ``*.hdf``, ``*.hdf5``."""
extensions = [
"h5",
"nc",
diff --git a/src/caosadvancedtools/json_schema_exporter.py b/src/caosadvancedtools/json_schema_exporter.py
index 3ac5247d85e3e3d5bca3f74d2033b7f258654d84..c36c9d0b1676b2486a44cad12fdcdcf03a24e806 100644
--- a/src/caosadvancedtools/json_schema_exporter.py
+++ b/src/caosadvancedtools/json_schema_exporter.py
@@ -575,8 +575,8 @@ def recordtype_to_json_schema(rt: db.RecordType, additional_properties: bool = T
wrap_files_in_objects : bool, optional
Whether (lists of) files should be wrapped into an array of objects that
have a file property. The sole purpose of this wrapping is to provide a
- workaround for a `react-jsonschema-form
- bug<https://github.com/rjsf-team/react-jsonschema-form/issues/3957>`_ so
+ workaround for a `react-jsonschema-form bug
+ <https://github.com/rjsf-team/react-jsonschema-form/issues/3957>`_ so
only set this to True if you're using the exported schema with
react-json-form and you are experiencing the bug. Default is False.
diff --git a/src/caosadvancedtools/serverside/generic_analysis.py b/src/caosadvancedtools/serverside/generic_analysis.py
index 85d0c860df75fce205c5eaad77731fc04eee9e40..7c7b26cc3ddb19ff54710f04debe3c0a48f35b82 100644
--- a/src/caosadvancedtools/serverside/generic_analysis.py
+++ b/src/caosadvancedtools/serverside/generic_analysis.py
@@ -38,7 +38,7 @@ Das aufgerufene Skript kann beliebige Eigenschaften benutzen und erstellen.
ABER wenn die Standardeigenschaften (InputDataSet, etc) verwendet werden, kann
der Record leicht erzeugt werden.
-
+.. code-block::
"Analyze" "Perform Anlysis"
Knopf an Record Form im WebUI
diff --git a/src/caosadvancedtools/suppressKnown.py b/src/caosadvancedtools/suppressKnown.py
index c4b57039c5184f2443e4dbb91cf11f5e59ae6790..1b31de7e9d8f1fdce35a135d558dd5ceea3bca2a 100644
--- a/src/caosadvancedtools/suppressKnown.py
+++ b/src/caosadvancedtools/suppressKnown.py
@@ -16,8 +16,11 @@ class SuppressKnown(logging.Filter):
added to the appropriate Logger and logging calls (e.g. to warning, info
etc.) need to have an additional `extra` argument.
This argument should be a dict that contains an identifier and a category.
- Example: `extra={"identifier":"<Record>something</Record>",
- category="entities"}
+
+ Example::
+
+ extra={"identifier":"<Record>something</Record>", category="entities"}
+
The identifier is used to check whether a message was shown before and
should be a string. The category can be used to remove a specific group of
messages from memory and the logger would show those messages again even
@@ -74,9 +77,7 @@ class SuppressKnown(logging.Filter):
return sha256((txt+str(identifier)).encode("utf-8")).hexdigest()
def filter(self, record):
- """
- Return whether the record shall be logged.
-
+ """Return whether the record shall be logged.
If either identifier of category is missing 1 is returned (logging
enabled). If the record has both attributes, it is checked whether the
diff --git a/src/caosadvancedtools/utils.py b/src/caosadvancedtools/utils.py
index 4d6a4b36bcb5dbdcd5bfe9357c53d4e9aa3501ca..05000a34fd27162837ecfe316b20af42b1156c45 100644
--- a/src/caosadvancedtools/utils.py
+++ b/src/caosadvancedtools/utils.py
@@ -113,17 +113,22 @@ def read_field_as_list(field):
return [field]
-def get_referenced_files(glob, prefix=None, filename=None, location=None):
+def get_referenced_files(glob: str, prefix: str = None, filename: str = None, location: str = None):
"""
queries the database for files referenced by the provided glob
- Parameters:
- glob: the glob referencing the file(s)
- prefix: the glob can be relative to some path, in that case that path needs
- to be given as prefix
- filename: the file in which the glob is given (used for error messages)
- location: the location in the file in which the glob is given (used for
- error messages)
+ Parameters
+ ----------
+ glob: str
+ the glob referencing the file(s)
+ prefix: str, optional
+ the glob can be relative to some path, in that case that path needs
+ to be given as prefix
+ filename: str, optional
+ the file in which the glob is given (used for error messages)
+ location: str, optional
+ the location in the file in which the glob is given (used for
+ error messages)
"""
orig_glob = glob
@@ -161,16 +166,19 @@ def get_referenced_files(glob, prefix=None, filename=None, location=None):
return files
-def check_win_path(path, filename=None):
+def check_win_path(path: str, filename: str = None):
"""
check whether '/' are in the path but no '\'.
If that is the case, it is likely, that the path is not a Windows path.
- Parameters:
- path: path to be checked
- filename: if the path is located in a file, this parameter can be used to
- direct the user to the file where the path is located.
+ Parameters
+ ----------
+ path: str
+ Path to be checked.
+ filename: str
+ If the path is located in a file, this parameter can be used to
+ direct the user to the file where the path is located.
"""
if r"\\" not in path and "/" in path:
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 37397f244ab05d4ad002569e2af2082530dab89f..db77cd7134d6eb1480da7f4b0674026c6255ed17 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -199,3 +199,7 @@ autodoc_default_options = {
'members': None,
'undoc-members': None,
}
+autodoc_mock_imports = [
+ "caosadvancedtools.bloxberg",
+ "labfolder",
+]