codespell: config, workflow + typos fixed (#541)

* Add github action to codespell master on push and PRs

* Add rudimentary codespell config

* add ignores

* [DATALAD RUNCMD] another ambigous typo fix

=== Do not change lines below ===
{
 "chain": [
  "3d3c4056c52ea0763b0a444fa980e8eac23bd99e"
 ],
 "cmd": "git-sedi retrival retrieval",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* ignore connexion module and zoon and rime and covert

* [DATALAD RUNCMD] run codespell throughout

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.ts,*.tsx,package-lock.json,data-*vocabulary.txt
+# regexes
+ignore-regex = r"\(\?i\).*\\\\1
+ignore-words-list = te,fwe,connexion,zoon,covert,rime

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+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

compose/README.md

@@ -9,7 +9,7 @@ First, set up the main environment variables in `.env` (see: `.env.example`).
 
 Edit the `.env` template to set the correct variables
 
-## Initalizing backend
+## Initializing backend
 Create the network, build the containers, and start services using the development configuration:
 
     docker network create nginx-proxy  # if this does not already exist

compose/neurosynth-frontend/src/assets/config/meta_analysis_params.json

@@ -155,7 +155,7 @@
                     "default": 10000
                 },
                 "xyz": {
-                    "description": "Tab-delimited file of coordinates from database or numpy array with XYZ coordinates. Voxels are rows and x, y, z (meaning coordinates) values are the three columnns.",
+                    "description": "Tab-delimited file of coordinates from database or numpy array with XYZ coordinates. Voxels are rows and x, y, z (meaning coordinates) values are the three columns.",
                     "type": "str",
                     "default": null
                 },

compose/neurosynth_compose/schemas/analysis.py

@@ -197,7 +197,7 @@ class MetaAnalysisResultSchema(BaseSchema):
 
     @post_load
     def process_data(self, data, **kwargs):
-        # propogate meta-analysis id to the neurovault collection
+        # propagate meta-analysis id to the neurovault collection
         if data.get("neurovault_collection", None):
             data["neurovault_collection"]["meta_analysis_id"] = data["meta_analysis_id"]
 

compose/neurosynth_compose/tests/conftest.py

@@ -155,7 +155,7 @@ def mock_ns(monkeysession):
 
 
 """
-Session / db managment tools
+Session / db management tools
 """
 
 

docs/taxonomy.md

@@ -45,7 +45,7 @@ The study is connected to the original journal it was published in.
 
 ### Functions
 
-Studies can be created, cloned, and edited to accomodate your needs for your meta-analysis
+Studies can be created, cloned, and edited to accommodate your needs for your meta-analysis
 
 ## Analysis
 

docs/typical-workflows.md

@@ -12,7 +12,7 @@ If the study does indeed use a finger tapping task, she wants to keep track of t
 To the left of the study there is a plus button.
 She clicks on the plus button and sees she can add the study to a "study-set".
 She names the studyset "finger tapping" and adds the selected study.
-When she is done reading and adding all relevent studies, she notices
+When she is done reading and adding all relevant studies, she notices
 that the finger tapping task typically falls under three categories:
 1) right handed index finger,
 2) right handed multiple fingers, and

store/README.md

@@ -9,7 +9,7 @@ First, set up the main environment variables in `.env` (see: `.env.example`).
 
 Edit the `.env` template to set the correct variables
 
-## Initalizing backend
+## Initializing backend
 Create the network, build the containers, and start services using the development configuration:
 
     docker network create nginx-proxy

store/neurostore/ingest/__init__.py

@@ -221,7 +221,7 @@ def ingest_neurosynth(max_rows=None):
                     base_study = base_studies[0]
                 elif len(base_studies) > 1:
                     source_base_study = base_studies[0]
-                    # do not overwrite the verions column
+                    # do not overwrite the versions column
                     # we want to append to this column
                     columns = [
                         c

store/neurostore/tests/api/test_conditions.py

@@ -5,7 +5,7 @@ def test_get_conditions(auth_client, ingest_neurovault):
 
 
 def test_post_conditions(auth_client, ingest_neurovault):
-    my_condition = {"name": "ice cream", "description": "suprise, it's rocky road!"}
+    my_condition = {"name": "ice cream", "description": "surprise, it's rocky road!"}
     post_resp = auth_client.post("/api/conditions/", data=my_condition)
     assert post_resp.status_code == 200
     post_data = post_resp.json

store/neurostore/tests/conftest.py

@@ -60,7 +60,7 @@ def mock_auth(monkeysession):
 
 
 """
-Session / db managment tools
+Session / db management tools
 """
 
 

store/neurostore/tests/test_schemas.py

@@ -16,7 +16,7 @@ def test_StudySchema(auth_client, ingest_neurosynth):
     StudySchema().validate(payload)
 
 
-@pytest.mark.skip(reason="website convienence parameters and exported object diverged")
+@pytest.mark.skip(reason="website convenience parameters and exported object diverged")
 def test_compare_dataset_with_snapshot(ingest_neurosynth):
     studyset = Studyset.query.first()
     marshmallow_ss = StudysetSchema(context={"nested": True, "copy": True}).dump(