Merge pull request #96 from yarikoptic/enh-codespell

add codespell: configuration, workflow + get it to fix found typos

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

README.md

@@ -180,7 +180,7 @@ and execute "python -m pasta_eln.test"
 
 #### HOW TO DIFF Version-1 and Version-2
 **COMPARE BOTH DIRECTIONS**
-at .. pasta-eln$ and remeber the changes required to Version2 in first change. If nothing to remember, do not execute 2nd command
+at .. pasta-eln$ and remember the changes required to Version2 in first change. If nothing to remember, do not execute 2nd command
 ``` bash
 kdiff pasta_eln/miscTools.py ../Python/miscTools.py
 kdiff ../Python/miscTools.py pasta_eln/miscTools.py

docs/source/faqs.rst

@@ -51,7 +51,7 @@ Implementation
         - no lock-in by software, software-architecture
     - Best version
         - A scientist has a desktop-based version that uploads the data to central servers.
-        - Supervisors, guests can use the webbased version to see the meta-data
+        - Supervisors, guests can use the web-based version to see the meta-data
         - The database can be filled with a command-line-interface (CLI), desktop program or cellphone.
         - Similar to 'git' which is the standard for distributed development.
 
@@ -62,7 +62,7 @@ Implementation
 *Why is the software for some users fast and for others slow?*
     We are aware of different run-times in different operating system. A backend test has different execution times on Windows (Thinkpad E495: 57.9sec), macOS (Macbook Air 2020: 20.8sec) and Linux (Thinkpad E495: 14.8sec). The graphical user interface seems to work similarly fast on all operating systems. We will investigate how to speed up the backend for Windows users in the future.
 
-*Why dont' you package everything in a flatpak or snap?*
+*Why don't you package everything in a flatpak or snap?*
     Containerization is a great concept for many software as it separates the host operating system from the software. This concept is not for PASTA-ELN because we require and want to extend extractors [See ...](extractors.md). As such the user/scientist should be able to change code and require libraries that are not included by default. These libraries cannot be added to the container. Scientist developed extractors cannot be archived in a container which should be self-sufficient and encapsulated. (Also, one could think of creating detours via system-calls / demons on the host system. However, flatpak and snap severely restrict host system-calls and cannot interact with processes on the host system.)
 
 Why does PASTA-ELN work in the way it does?

docs/source/motivation.rst

@@ -128,7 +128,7 @@ All documents have the following properties
 - type is a list of hierarchical types:
   - examples for most data: ["measurement", "Zeiss tif image"], ["measurement", "Indentation", "Pop-in study"]
   - text items (projects, tasks) are ["x0"], ["x1"], ... as the types are non hierarchical in the class view (IT-term). A task is not a special class of the project class. Moreover, the hierarchical level is ingrained in the type
-- Tags #tag, #1 (no spaces in the string). #1 implies one-star, #2 implies two-stars. Tags are stored as list of stings.
+- Tags #tag, #1 (no spaces in the string). #1 implies one-star, #2 implies two-stars. Tags are stored as list of strings.
 - other fields can be easily added in the comment field of the form and are thereafter separated. Examples for other fields:  :BakingTime:2h: :quality:3:  (':' is a marker here)
 - Comments
   - If the user enters a comment in the comment field: tags and fields are subtracted and everything that remains is the comment

pasta_eln/GUI/config.py

@@ -34,7 +34,7 @@ def __init__(self, comm:Communicate, startTab:str=''):
     tabGUI = ConfigurationAuthors(self.comm, self.finished)
     tabW.addTab(tabGUI, 'Authors')
 
-    # Setup / Troubeshoot Pasta: main widget
+    # Setup / Troubleshoot Pasta: main widget
     tabSetup = ConfigurationSetup(self.comm, self.finished)
     tabW.addTab(tabSetup, 'Setup')
 

pasta_eln/GUI/configSetupLinux.py

@@ -51,7 +51,7 @@ def __init__(self, comm:Communicate, callbackFinished:Callable[[],None]):
 
   def callbackProgress(self, number:int) -> None:
     """
-    Increse progressbar by moving to number
+    Increase progressbar by moving to number
 
     Args:
       number (int): integer to move to

pasta_eln/GUI/configSetupWindows.py

@@ -49,7 +49,7 @@ def __init__(self, comm:Communicate, callbackFinished:Callable[[],None]):
 
   def callbackProgress(self, number:int) -> None:
     """
-    Increse progressbar by moving to number
+    Increase progressbar by moving to number
 
     Args:
       number (int): integer to move to

pasta_eln/GUI/ontology_configuration/ontology_props_tableview_data_model.py

@@ -79,7 +79,7 @@ def data(self,
            index: Union[QModelIndex, QPersistentModelIndex],
            role: int = Qt.ItemDataRole) -> Any:  # type: ignore[assignment]
     """
-    Overriden method for getting the data, only handles the PROPS_TABLE_LIST_COLUMN_INDEX case
+    Overridden method for getting the data, only handles the PROPS_TABLE_LIST_COLUMN_INDEX case
     Args:
       index (Union[QModelIndex, QPersistentModelIndex]): Table cell index
       role (int): Role for the data

pasta_eln/GUI/projectGroup.py

@@ -1,4 +1,4 @@
-""" Table Header dialog: change which colums are shown and in which order """
+""" Table Header dialog: change which columns are shown and in which order """
 import json, platform
 from enum import Enum
 from pathlib import Path
@@ -14,7 +14,7 @@
 from ..guiCommunicate import Communicate
 
 class ProjectGroup(QDialog):
-  """ Table Header dialog: change which colums are shown and in which order """
+  """ Table Header dialog: change which columns are shown and in which order """
   def __init__(self, comm:Communicate):
     """
     Initialization

pasta_eln/GUI/table.py

@@ -143,7 +143,7 @@ def change(self, docType:str, projID:str) -> None:
       self.showHidden.setText(f'Show/hide hidden {docLabel.lower()}')
       self.filterHeader = self.comm.backend.db.getColumnNames()[self.docType].split(',')
       self.filterHeader = [i[1:] if i[0]=='-'   else i for i in self.filterHeader]  #change -something to something
-      self.filterHeader = [i[2:] if i[:2]=='#_' else i for i in self.filterHeader]  #change #_something to somehing
+      self.filterHeader = [i[2:] if i[:2]=='#_' else i for i in self.filterHeader]  #change #_something to something
     self.headerW.show()
     nrows, ncols = len(self.data), len(self.filterHeader)
     model = QStandardItemModel(nrows, ncols)

pasta_eln/GUI/tableHeader.py

@@ -1,4 +1,4 @@
-""" Table Header dialog: change which colums are shown and in which order """
+""" Table Header dialog: change which columns are shown and in which order """
 from enum import Enum
 from typing import Any
 from PySide6.QtWidgets import QDialog, QVBoxLayout, QListWidget, QLineEdit, QDialogButtonBox  # pylint: disable=no-name-in-module
@@ -8,7 +8,7 @@
 from ..fixedStringsJson import tableHeaderHelp
 
 class TableHeader(QDialog):
-  """ Table Header dialog: change which colums are shown and in which order """
+  """ Table Header dialog: change which columns are shown and in which order """
   def __init__(self, comm:Communicate, docType:str):
     """
     Initialization

pasta_eln/cli.py

@@ -325,7 +325,7 @@ def main() -> None:
   usage+= commands(True, argparse.Namespace())
   argparser = argparse.ArgumentParser(usage=usage)
   argparser.add_argument('command', help='see above...')
-  argparser.add_argument('-i','--docID',   help='docID of project; a long alpha-numeric code', default='')
+  argparser.add_argument('-i','--docID',   help='docID of project; a long alphanumeric code', default='')
   argparser.add_argument('-c','--content', help='content to save/store', default=None)
   argparser.add_argument('-l','--label',   help='label used for printing', default='x0')
   argparser.add_argument('-d','--database',help='name of database configuration', default='') #required for be = Pasta(args.database)

pasta_eln/database.py

@@ -223,7 +223,7 @@ def saveDoc(self, doc:dict[str,Any]) -> dict[str,Any]:
     - full path (from basePath) allows to easily create a view of all paths and search through them
       during each scan, which happens rather often
     - just the incremental path (file-name, folder-name) allows to easily change that if the user wants
-      and not change all the children paths, too. However, the renaming of the folder is likely occuring
+      and not change all the children paths, too. However, the renaming of the folder is likely occurring
       less often.
 
     Args:
@@ -348,7 +348,7 @@ def updateDoc(self, change:dict[str,Any], docID:str) -> dict[str,Any]:
           elif item in newDoc:
             oldDoc[item] = newDoc[item]
           newDoc[item] = change[item]
-      # Always update, for some reason single tags are not recongnized
+      # Always update, for some reason single tags are not recognized
       # if nothingChanged:
       #   logging.debug('database.update.2: doc not updated-nothing changed: '+newDoc['_id']+' '+newDoc['-name'])
       #   return newDoc
@@ -720,7 +720,7 @@ def historyDB(self) -> dict[str,Any]:
       if np.min(value) < firstSubmit:
         firstSubmit = np.min(value)
     bins = np.linspace(firstSubmit, datetime.now().timestamp(), 100 )
-    #calculate histgram and save it
+    #calculate histogram and save it
     collectionCopy = dict(collection)
     for key,value in collection.items():
       hist, _ = np.histogram(value, bins)

pasta_eln/gui.py

@@ -235,7 +235,7 @@ def mainGUI() -> tuple[Union[QCoreApplication, None], MainWindow]:
   if not isinstance(qta.icon('fa5s.times'), QIcon):
     logging.error('qtawesome: could not load. Likely matplotlib is included and can not coexist.')
     print('qtawesome: could not load. Likely matplotlib is included and can not coexist.')
-  # end test coexistance
+  # end test coexistence
   logging.info('End PASTA GUI')
   return application, main_window
 

pasta_eln/handleDictionaries.py

@@ -66,7 +66,7 @@ def ontologyV2_to_V3(ontology: dict[str, Any]) -> None:
 
 def fillDocBeforeCreate(data:dict[str,Any], docType:list[str]) -> dict[str,Any]:
   """ Fill the data before submission to database with common data
-  - type, project, childs
+  - type, project, children
   - separate comment into tags, fields
   - create id if needed
 
@@ -101,7 +101,7 @@ def fillDocBeforeCreate(data:dict[str,Any], docType:list[str]) -> dict[str,Any]:
     data['comment'] =''
   if '-tags' not in data:
     data['-tags'] = []
-  #always do regex expressions twice: if #lala at beginnig or in middle of comment
+  #always do regex expressions twice: if #lala at beginning or in middle of comment
   curated = re.findall(r'(?:^|\s)#_curated(?:\s|$)', data['comment']) # #_curated
   rating  = re.findall(r'(?:^|\s)#_\d(?:\s|$)',      data['comment']) # #_number
   if rating is None:

pasta_eln/miscTools.py

@@ -34,7 +34,7 @@ def outputString(fmt:str='print', level:str='info', message:str='') -> str:
   """ Output a message into different formats:
     - print: print to stdout
     - logging; log to file
-    - text: return text string (superseeds html)
+    - text: return text string (supersedes html)
     - html: return html string https://doc.qt.io/qtforpython/overviews/richtext-html-subset.html#supported-html-subset
     - else: no output
     - formats can be union ('print,text')

pasta_eln/serverActions.py

@@ -328,7 +328,7 @@ def listDocuments(url:str, userName:str, password:str, database:str, full:bool=T
 
 def backupCouchDB(location:str='', userName:str='', password:str='') -> None:
   """
-  Backup everything of the CouchDB installation accross all databases and all configurations
+  Backup everything of the CouchDB installation across all databases and all configurations
   - remote location uses username/password combo in local keystore
   - local location requires username and password
 
@@ -406,7 +406,7 @@ def backupCouchDB(location:str='', userName:str='', password:str='') -> None:
 
 def restoreCouchDB(location:str='', userName:str='', password:str='', fileName:str='') -> None:
   """
-  restore everything to the CouchDB installation accross all databases and all configurations
+  restore everything to the CouchDB installation across all databases and all configurations
   - remote location uses username/password combo in local keystore
   - local location requires username and password
 
@@ -485,7 +485,7 @@ def restoreCouchDB(location:str='', userName:str='', password:str='', fileName:s
       docID = fileParts[1]
       if not docID.endswith('_attach'):
         continue #Did already in the first loop
-      #test if attachement exists: create otherwise
+      #test if attachment exists: create otherwise
       attachPath = f'{docID[:-7]}/{fileParts[-1]}'
       resp = requests.get(f'http://{location}:5984/{database}/{attachPath}', headers=headers, auth=authUser, timeout=10)
       if resp.status_code == 404 and 'missing' in resp.json()['reason']:

pyproject.toml

@@ -1,2 +1,9 @@
 [build-system]
 requires = ["setuptools >= 43.0.0", "wheel"]
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,*lookup*.json'
+# for shortcuts like [l]ist
+ignore-regex = '\[[a-z]\][a-z]+'
+#
+ignore-words-list = 'speciall,ons,crate,ser'

tests/app_tests/component_tests/test_ontology_configuration_extended.py

@@ -878,7 +878,7 @@ def test_re_order_property_table_should_work_as_expected(self,
     assert ui_form.propsCategoryComboBox.currentText() == "default", f"propsCategoryComboBox.currentText() should be default!"
     model = ui_form.typePropsTableView.model()
     assert model.rowCount() == 5, "5 properties must be present before deletion!"
-    # Initial data oder
+    # Initial data order
     init_data_order = ['-name', 'status', 'objective', '-tags', 'comment']
     post_reorder_data_order1 = ['-name', 'status', 'objective', 'comment', '-tags']
     post_reorder_data_order2 = ['status', '-name', 'objective', 'comment', '-tags']