Codespell - edit typos (#1189)

* correct spelling in CHANGELOG.rst

* edit typos

* add tool.codespell section to pyproject.toml

* add ignore_lines and ignore_words

* add ignore_words

* add codespell to pre-commit

* add more file extensions to skip

* fix typo

* add more words to ignore

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,26 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro
+
+;; variable names
+stati
+convertor
+dploy
+pres
+
+;; package name
+rever
+
+;; people.rst manually allows 'programer' as a variation of 'programmer'
+programer
+
+;; suffix for dates
+nd

.pre-commit-config.yaml

@@ -44,3 +44,9 @@ repos:
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli

CHANGELOG.rst

@@ -314,7 +314,7 @@ v0.3.1
 
 **Changed:**
 
-* ``open`` uses explict 'utf-8' bindings (for windows users)
+* ``open`` uses explicit 'utf-8' bindings (for windows users)
 * Allow education to be ongoing
 * Allow begin and end years for service
 * Make employment optional
@@ -434,7 +434,7 @@ v0.2.0
 
 * Error in ``BaseBuilder`` which caused it to look in the wrong spot for
   templates
-* Fixed bug in grad builder when the total wieght is zero.
+* Fixed bug in grad builder when the total weight is zero.
 * Actually use ``ChainedDB`` when working with the DBs
 
 * Error in ``ChainedDB`` which caused bad keys to return with ``None``
@@ -465,7 +465,7 @@ v0.1.10
 
 **Changed:**
 
-* ``CVBuilder`` and ``ResumeBuilder`` builders now inheret from ``LatexBuilderBase``
+* ``CVBuilder`` and ``ResumeBuilder`` builders now inherit from ``LatexBuilderBase``
 
 
 **Fixed:**

README.rst

@@ -120,7 +120,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/regro/regolith/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/regro/regolith/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------

doc/source/collections/beamplan.rst

@@ -57,7 +57,7 @@ YAML Example
 	  exp_plan:
 	    - load samples on the holder
 	    - scan the holder to locate the samples
-	    - take room temperature measurement of sample and the subtrate
+	    - take room temperature measurement of sample and the substrate
 	    - ramp down temperature to 100K
 	    - ramp up, measure PDF at temperature 100K ~ 300K, 10K stepsize, 1 min exposure
 	  holder: film holder (1 cm * 1 cm * 1 mm)
@@ -70,7 +70,7 @@ YAML Example
 	  project_lead: kseth
 	  samples:
 	    - WO3 film
-	    - glass subtrate
+	    - glass substrate
 	  scanplan:
 	    - Scanplan(bt, Tramp, 30, 80, 500, 10)
 	  ship_plan:
@@ -97,7 +97,7 @@ JSON/Mongo Example
 	    "exp_plan": [
 	        "load samples on the holder",
 	        "scan the holder to locate the samples",
-	        "take room temperature measurement of sample and the subtrate",
+	        "take room temperature measurement of sample and the substrate",
 	        "ramp down temperature to 100K",
 	        "ramp up, measure PDF at temperature 100K ~ 300K, 10K stepsize, 1 min exposure"
 	    ],
@@ -112,7 +112,7 @@ JSON/Mongo Example
 	    "project_lead": "kseth",
 	    "samples": [
 	        "WO3 film",
-	        "glass subtrate"
+	        "glass substrate"
 	    ],
 	    "scanplan": [
 	        "Scanplan(bt, Tramp, 30, 80, 500, 10)"

doc/source/commands/classlist.rst

@@ -7,7 +7,7 @@ classlist
 	                          op filename course_id
 
 	positional arguments:
-	  op                    operatation to perform, such as "add" or "replace".
+	  op                    operation to perform, such as "add" or "replace".
 	  filename              file to read class information from.
 	  course_id             course identifier whose registry should be updated
 

doc/source/commands/ingest.rst

@@ -11,5 +11,5 @@ ingest
 
 	options:
 	  -h, --help   show this help message and exit
-	  --coll COLL  collection name, if this is not given it is infered from the
+	  --coll COLL  collection name, if this is not given it is inferred from the
 	               file type or file name.

doc/source/database_maintenance/mongo_maintenance.rst

@@ -47,7 +47,7 @@ Setting Up a Server
 **LOCAL**
 
 | Your local server is automatically running as a service on localhost if you have downloaded the community version of
-  mongodb correctly. **Congradulations!**
+  mongodb correctly. **Congratulations!**
 
 | Accessing your local mongodb server **for administrative purposes** can be done simply by typing "mongo" into your
   terminal, which opens the mongodb shell. By default, you will have three databases present (admin, config, local).

doc/source/rc.rst

@@ -111,7 +111,7 @@ The MongoDB client to use.  This is almost always set by regolith internally.
 
 ``db``
 =========
-The database to use.  This should coorespond to the name field of one of the ``databases`` entries.
+The database to use.  This should correspond to the name field of one of the ``databases`` entries.
 
 ``coll``
 =========
@@ -128,7 +128,7 @@ Boolean for whether to select only public databases.
 
 ``filename``
 ==============
-Sting that is a path to a file to operate on.
+String that is a path to a file to operate on.
 
 ``debug``
 ================

pyproject.toml

@@ -91,3 +91,8 @@ exclude = '''
   | tests/data
 )/
 '''
+
+[tool.codespell]
+exclude-file = ".codespell/ignore_lines.txt"
+ignore-words = ".codespell/ignore_words.txt"
+skip = "*.cif, *.dat, *.js, *.txt, *.map, *.tex, *.bib, *.json, *.html"

src/regolith/broker.py

@@ -23,7 +23,7 @@ class Broker:
 
     >>> # Load the db
     >>> db = Broker.from_rc()
-    >>> # Get a docment from the broker
+    >>> # Get a document from the broker
     >>> ergs =db['group']['ergs']
     >>> # Store a file
     >>> db.add_file(ergs, 'myfile', '/path/to/file/hello.txt')

src/regolith/builders/coabuilder.py

@@ -2,7 +2,7 @@
 
 For the specified person it returns the name and institution of all
 graduate student and post-doc advisors,
-all graduate student advisees, all post-doc advisees in the past 60 monts
+all graduate student advisees, all post-doc advisees in the past 60 months
 and all coauthors in the past 48 months.
 """
 
@@ -253,7 +253,7 @@ def query_people_and_institutions(rc, names):
 
 
 def get_inst_name(person, rc):
-    """Get the name of instituion of the person's latest employment."""
+    """Get the name of institution of the person's latest employment."""
     if "employment" in person:
         org = get_recent_org(person)
         person_inst_abbr = org

src/regolith/client_manager.py

@@ -97,13 +97,13 @@ def keys(self):
         return keys
 
     def collection_names(self, dbname, include_system_collections=True):
-        """Returns the collaction names for a database."""
+        """Returns the collection names for a database."""
         for client in self.clients:
             if dbname in client.keys():
                 return client.collection_names(dbname)
 
     def all_documents(self, collname, copy=True):
-        """Returns an iteratable over all documents in a collection."""
+        """Returns an iterable over all documents in a collection."""
         if copy:
             return deepcopy(self.chained_db.get(collname, {})).values()
         return self.chained_db.get(collname, {}).values()

src/regolith/emailer.py

@@ -39,8 +39,8 @@ def attach_pdf(filename):
 
 
 def make_message(rc, to, subject="", body="", attachments=()):
-    """Creates an email following the approriate format. The body kwarg
-    may be a string of restructured text.  Attachements is a list of filenames
+    """Creates an email following the appropriate format. The body kwarg
+    may be a string of restructured text.  Attachments is a list of filenames
     to attach.
     """
     msg = MIMEMultipart("alternative")

src/regolith/fsclient.py

@@ -229,11 +229,11 @@ def __getitem__(self, key):
         return self.dbs[key]
 
     def collection_names(self, dbname, include_system_collections=True):
-        """Returns the collaction names for a database."""
+        """Returns the collection names for a database."""
         return set(self.dbs[dbname].keys())
 
     def all_documents(self, collname, copy=True):
-        """Returns an iteratable over all documents in a collection."""
+        """Returns an iterable over all documents in a collection."""
         if copy:
             return deepcopy(self.chained_db.get(collname, {})).values()
         return self.chained_db.get(collname, {}).values()

src/regolith/helper.py

@@ -52,7 +52,7 @@
     "u_todo": (u_todo.TodoUpdaterHelper, u_todo.subparser),
 }
 
-# Lister helpers need to load collections across all the databses to show everything
+# Lister helpers need to load collections across all the databases to show everything
 LISTER_HELPERS = {
     "l_abstract": (l_abstract.AbstractListerHelper, l_abstract.subparser),
     "l_contacts": (l_contacts.ContactsListerHelper, l_contacts.subparser),

src/regolith/helpers/a_projectumhelper.py

@@ -233,7 +233,7 @@ def insert_checklists(self, pdoc, now):
         presubmission_checklist = [
             (
                 "Create slide figures",
-                "Create Inkscape graphics (Inkscape is preferrable over ppt) for the slides "
+                "Create Inkscape graphics (Inkscape is preferable over ppt) for the slides "
                 "and place in a ``figures`` directory in the slides directory. "
                 "These may then be used either in beamer or ppt. "
                 "Iterate with PI to convergence. (to get started with Inkscape download and install it, "
@@ -581,7 +581,7 @@ def insert_checklists(self, pdoc, now):
                 "Read the paper",
                 "Finally, after you have done all these 'mechanical' checks, "
                 "read through the paper and try and find any typos or other problems. "
-                "Resist the temptation to do any rewriting here...you are looking for mispellings "
+                "Resist the temptation to do any rewriting here...you are looking for misspellings "
                 "and missing or extra words and so on.",
             ),
             (
@@ -693,7 +693,7 @@ def insert_checklists(self, pdoc, now):
                 "Update arXiv if necessary",
                 "If the paper was listed on a preprint server like arXiv, submit a note to arXiv that the paper "
                 "has appeared and give the full reference. If the journal copyright allows "
-                "you can post the published version here, but normally that is not alllowed! "
+                "you can post the published version here, but normally that is not allowed! "
                 "Still, it is important that people who find the paper on arXiv "
                 "get directed to the correct reference.",
             ),
@@ -831,7 +831,7 @@ def insert_checklists(self, pdoc, now):
         #                                 'closes.  The goal of this is that it will be '
         #                                 'printed as a progress report for a grant '
         #                                 'so write it as if it will be read by an external '
-        #                                 'person. It doesnt have to describe the whole prum '
+        #                                 'person. It doesn't have to describe the whole prum '
         #                                 'but clearly show the progress that has been made. '
         #                                 'It can be multiple paragraphs or a short statement'
         #                                 'depending on the situation',

src/regolith/helpers/attestationshelper.py

@@ -86,7 +86,7 @@ def db_updater(self):
             print(rc.begin_date)
             raise RuntimeError(
                 "Begin date needed for effort reporting.  Please rerun specifying "
-                "--begin-date YYYY-MM-DD (and preferrably --end-date YYYY-MM-DD) "
+                "--begin-date YYYY-MM-DD (and preferably --end-date YYYY-MM-DD) "
                 "or remove --effort-reporting if you "
                 "want an attestation report for a grant"
             )

src/regolith/main.py

@@ -55,7 +55,7 @@ def create_parser():
         "--coll",
         dest="coll",
         default=None,
-        help="collection name, if this is not given it is infered from the " "file type or file name.",
+        help="collection name, if this is not given it is inferred from the " "file type or file name.",
     )
 
     # store subparser

src/regolith/runcontrol.py

@@ -248,7 +248,7 @@ def load_rcfile(fname):
     if ext == ".json":
         rc = load_json_rcfile(fname)
     else:
-        raise RuntimeError("could not detemine run control file type from extension.")
+        raise RuntimeError("could not determine run control file type from extension.")
     return rc
 
 

src/regolith/schemas.py

@@ -161,7 +161,7 @@ def load_exemplars():
 for s in SCHEMAS:
     SCHEMAS[s]["files"] = {
         "description": "Files associated with the document",
-        # TODO: fix this since this is currently comming out a CommentedMap (+1: Yevgeny)
+        # TODO: fix this since this is currently coming out a CommentedMap (+1: Yevgeny)
         # "type": "list",
         # "schema": {"type": "string"},
         "required": False,

src/regolith/tests/test_builders.py

@@ -149,7 +149,7 @@ def test_builder(bm, db_src, make_db, make_mongodb, monkeypatch):
     for testfile in test_files:
         if testfile.name not in output_filenames:
             print(
-                f"Expected test file {testfile} not generated by the builder." f"Files genereated: {output_files}"
+                f"Expected test file {testfile} not generated by the builder." f"Files generated: {output_files}"
             )
             assert False
     # for all other test output 'expected' files check they are the same as the program output
@@ -280,7 +280,7 @@ def mockreturn(*args, **kwargs):
     for testfile in test_files:
         if testfile.name not in output_filenames:
             print(
-                f"Expected test file {testfile} not generated by the builder." f"Files genereated: {output_files}"
+                f"Expected test file {testfile} not generated by the builder." f"Files generated: {output_files}"
             )
             assert False
     # for all other test output 'expected' files check they are the same as the program output

src/regolith/tools.py

@@ -1195,7 +1195,7 @@ def get_person_contact(name, people_coll, contacts_coll):
 
 def merge_collections_intersect(a, b, target_id):
     """
-    merge two collections such thta just the intersection is returned
+    merge two collections such that just the intersection is returned
 
     for shared keys that are in both collections, the value in b will be kept
 
@@ -2211,7 +2211,7 @@ def get_target_token(target_token_id, tokens):
 
 
 def create_repo(destination_id, token_info_id, rc):
-    """Creates a repo at the target distination
+    """Creates a repo at the target destination
 
     tries to fail gracefully if repo information and token is not defined