diff --git a/doc/source/collections/beamplan.rst b/doc/source/collections/beamplan.rst index f381656d7..c9829139e 100644 --- a/doc/source/collections/beamplan.rst +++ b/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)" diff --git a/doc/source/commands/classlist.rst b/doc/source/commands/classlist.rst index dfd908d45..a3cfad87e 100644 --- a/doc/source/commands/classlist.rst +++ b/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 diff --git a/doc/source/commands/ingest.rst b/doc/source/commands/ingest.rst index a0e8b6bb3..4d08da493 100644 --- a/doc/source/commands/ingest.rst +++ b/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. diff --git a/doc/source/database_maintenance/mongo_maintenance.rst b/doc/source/database_maintenance/mongo_maintenance.rst index 9422739af..9c23aa55b 100644 --- a/doc/source/database_maintenance/mongo_maintenance.rst +++ b/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). diff --git a/doc/source/rc.rst b/doc/source/rc.rst index d03125964..665db3aec 100644 --- a/doc/source/rc.rst +++ b/doc/source/rc.rst @@ -15,12 +15,12 @@ The temporary location to build whatever it is needs building. ``mongodbpath`` ================ The value to pass into the ``--dbpath`` option to ``mongod``. Defaults to ``'${builddir}/_dbpath'`` -if unspecified. +if unspecified. ``databases`` =============== -This represents the public or private databases that are used to store unstructured data about the group +This represents the public or private databases that are used to store unstructured data about the group and its activities. .. code-block:: python @@ -39,7 +39,7 @@ and its activities. ``stores`` =============== -This is used to represent connection information to document stores, think PDFs, images, etc. +This is used to represent connection information to document stores, think PDFs, images, etc. .. code-block:: python @@ -60,7 +60,7 @@ This is a string of the research group name. ``cname`` ============ -This is a string of the CNAME value. This will be put into a file called CNAME in the root +This is a string of the CNAME value. This will be put into a file called CNAME in the root HTML build dir, if it is present. @@ -83,7 +83,7 @@ This is a list of deployment targets to send information to from the build direc ``deploydir`` ====================== -The temporary location to for all deployment directories. If not present, this +The temporary location to for all deployment directories. If not present, this will default to a ``deploy`` dir inside of the ``builddir`` .. code-block:: python @@ -93,12 +93,12 @@ will default to a ``deploy`` dir inside of the ``builddir`` --------------------------------- Keys Usually Set by CLI --------------------------------- -The following keys are normally set by the command line interface. However, you +The following keys are normally set by the command line interface. However, you can set them in the run control file should you choose to. ``cmd`` ========= -The command to run. +The command to run. .. code-block:: python @@ -111,11 +111,11 @@ 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`` ========= -The collection name inside of a database to use. +The collection name inside of a database to use. ``documents`` ================ @@ -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`` ================ diff --git a/src/regolith/broker.py b/src/regolith/broker.py index d58f73530..1c7b26f81 100644 --- a/src/regolith/broker.py +++ b/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') diff --git a/src/regolith/builders/coabuilder.py b/src/regolith/builders/coabuilder.py index 766fba389..c544eabc8 100644 --- a/src/regolith/builders/coabuilder.py +++ b/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 diff --git a/src/regolith/client_manager.py b/src/regolith/client_manager.py index 22038d099..3b9c792ec 100644 --- a/src/regolith/client_manager.py +++ b/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() diff --git a/src/regolith/emailer.py b/src/regolith/emailer.py index 079b2a872..0197827b3 100644 --- a/src/regolith/emailer.py +++ b/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") diff --git a/src/regolith/fsclient.py b/src/regolith/fsclient.py index 39d14cd45..37336ae82 100644 --- a/src/regolith/fsclient.py +++ b/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() diff --git a/src/regolith/helper.py b/src/regolith/helper.py index e3231d3ab..b23ba45cc 100644 --- a/src/regolith/helper.py +++ b/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), diff --git a/src/regolith/helpers/a_projectumhelper.py b/src/regolith/helpers/a_projectumhelper.py index 9ab4841a5..429aa28d5 100644 --- a/src/regolith/helpers/a_projectumhelper.py +++ b/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', diff --git a/src/regolith/helpers/attestationshelper.py b/src/regolith/helpers/attestationshelper.py index 0ca2ca0f5..5ad64bbc3 100644 --- a/src/regolith/helpers/attestationshelper.py +++ b/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" ) diff --git a/src/regolith/main.py b/src/regolith/main.py index 02c1dc110..ac2eeee35 100644 --- a/src/regolith/main.py +++ b/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 diff --git a/src/regolith/runcontrol.py b/src/regolith/runcontrol.py index f3b01223a..51a3fa5f7 100644 --- a/src/regolith/runcontrol.py +++ b/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 diff --git a/src/regolith/schemas.py b/src/regolith/schemas.py index 28e0e98d1..cc4ae76d1 100644 --- a/src/regolith/schemas.py +++ b/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, diff --git a/src/regolith/tests/test_builders.py b/src/regolith/tests/test_builders.py index 9db944aec..3fbb61809 100644 --- a/src/regolith/tests/test_builders.py +++ b/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 diff --git a/src/regolith/tools.py b/src/regolith/tools.py index a7e7e476e..b083f60ae 100644 --- a/src/regolith/tools.py +++ b/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