Merge pull request #44 from MilagrosMarin/main

Fix codespell and black formatting
datajoint · Jul 3, 2024 · 8b4b750 · 8b4b750
2 parents 008dccf + e21c53c
commit 8b4b750
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diff --git a/.codespellrc b/.codespellrc
@@ -1,5 +1,6 @@
 [codespell]
-skip = .git,*.pdf,*.svg
-ignore-regex = ^\s*"image/\S+": ".*
+skip=.git,*.pdf,*.svg,*.ipynb
+ignore-regex=^\s*"image/\S+": ".*
+
 #
-# ignore-words-list =
+ignore-words-list=shepard,nevers,nin,DaSy,Fo,Alle,ND
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -1,4 +1,3 @@
----
 name: Codespell
 
 on:
@@ -18,5 +17,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
+
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
diff --git a/completed_tutorials/01-DataJoint Basics.ipynb b/completed_tutorials/01-DataJoint Basics.ipynb
@@ -249,7 +249,7 @@
     }
    ],
    "source": [
-    "schema = dj.schema('tutorial')"
+    "schema = dj.schema(\"tutorial\")"
    ]
   },
   {
@@ -421,7 +421,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Mouse.insert1((0, '2017-03-01', 'M'))"
+    "Mouse.insert1((0, \"2017-03-01\", \"M\"))"
    ]
   },
   {
@@ -533,11 +533,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = {\n",
-    "    'mouse_id': 100,\n",
-    "    'dob': '2017-05-12',\n",
-    "    'sex': 'F'\n",
-    "}"
+    "data = {\"mouse_id\": 100, \"dob\": \"2017-05-12\", \"sex\": \"F\"}"
    ]
   },
   {
@@ -661,11 +657,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = [\n",
-    "  (1, '2016-11-19', 'M'),\n",
-    "  (2, '2016-11-20', 'unknown'),\n",
-    "  (5, '2016-12-25', 'F')\n",
-    "]"
+    "data = [(1, \"2016-11-19\", \"M\"), (2, \"2016-11-20\", \"unknown\"), (5, \"2016-12-25\", \"F\")]"
    ]
   },
   {
@@ -691,8 +683,8 @@
    "outputs": [],
    "source": [
     "data = [\n",
-    "    {'mouse_id': 10, 'dob': '2017-01-01', 'sex': 'F'},\n",
-    "    {'mouse_id': 11, 'dob': '2017-01-03', 'sex': 'F'},\n",
+    "    {\"mouse_id\": 10, \"dob\": \"2017-01-01\", \"sex\": \"F\"},\n",
+    "    {\"mouse_id\": 11, \"dob\": \"2017-01-03\", \"sex\": \"F\"},\n",
     "]\n",
     "\n",
     "# insert them all\n",
@@ -848,10 +840,12 @@
    ],
    "source": [
     "Mouse.insert1(\n",
-    "{'mouse_id': 0,\n",
-    " 'dob': '2018-01-01',\n",
-    " 'sex': 'M',\n",
-    "})"
+    "    {\n",
+    "        \"mouse_id\": 0,\n",
+    "        \"dob\": \"2018-01-01\",\n",
+    "        \"sex\": \"M\",\n",
+    "    }\n",
+    ")"
    ]
   },
   {
@@ -868,11 +862,11 @@
    "outputs": [],
    "source": [
     "data = [\n",
-    "    {'mouse_id': 12, 'dob': '2017-03-21', 'sex': 'F'},\n",
-    "    {'mouse_id': 18, 'dob': '2017-05-01', 'sex': 'F'},\n",
-    "    {'mouse_id': 19, 'dob': '2018-07-21', 'sex': 'M'},\n",
-    "    {'mouse_id': 22, 'dob': '2019-12-15', 'sex': 'F'},\n",
-    "    {'mouse_id': 34, 'dob': '2018-09-22', 'sex': 'M'}\n",
+    "    {\"mouse_id\": 12, \"dob\": \"2017-03-21\", \"sex\": \"F\"},\n",
+    "    {\"mouse_id\": 18, \"dob\": \"2017-05-01\", \"sex\": \"F\"},\n",
+    "    {\"mouse_id\": 19, \"dob\": \"2018-07-21\", \"sex\": \"M\"},\n",
+    "    {\"mouse_id\": 22, \"dob\": \"2019-12-15\", \"sex\": \"F\"},\n",
+    "    {\"mouse_id\": 34, \"dob\": \"2018-09-22\", \"sex\": \"M\"},\n",
     "]\n",
     "\n",
     "# insert them all\n",
@@ -1014,7 +1008,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ENTER YOUR CODE - Insert more mice\n"
+    "# ENTER YOUR CODE - Insert more mice"
    ]
   },
   {
@@ -1135,10 +1129,10 @@
    "outputs": [],
    "source": [
     "data = {\n",
-    "  'mouse_id': 0,\n",
-    "  'session_date': '2017-05-15',\n",
-    "  'experiment_setup': 0,\n",
-    "  'experimenter': 'Edgar Y. Walker'\n",
+    "    \"mouse_id\": 0,\n",
+    "    \"session_date\": \"2017-05-15\",\n",
+    "    \"experiment_setup\": 0,\n",
+    "    \"experimenter\": \"Edgar Y. Walker\",\n",
     "}\n",
     "\n",
     "Session.insert1(data)"
@@ -1362,10 +1356,10 @@
    ],
    "source": [
     "data = {\n",
-    "  'mouse_id': 0,\n",
-    "  'session_date': '2018-01-15',\n",
-    "  'experiment_setup': 100,\n",
-    "  'experimenter': 'Jacob Reimer'\n",
+    "    \"mouse_id\": 0,\n",
+    "    \"session_date\": \"2018-01-15\",\n",
+    "    \"experiment_setup\": 100,\n",
+    "    \"experimenter\": \"Jacob Reimer\",\n",
     "}\n",
     "\n",
     "Session.insert1(data)\n",
@@ -1387,10 +1381,10 @@
    "outputs": [],
    "source": [
     "data = {\n",
-    "  'mouse_id': 18,\n",
-    "  'session_date': '2018-01-15',\n",
-    "  'experiment_setup': 101,\n",
-    "  'experimenter': 'Jacob Reimer'\n",
+    "    \"mouse_id\": 18,\n",
+    "    \"session_date\": \"2018-01-15\",\n",
+    "    \"experiment_setup\": 101,\n",
+    "    \"experimenter\": \"Jacob Reimer\",\n",
     "}\n",
     "\n",
     "# insert them all\n",
@@ -1525,10 +1519,10 @@
    "outputs": [],
    "source": [
     "bad_data = {\n",
-    "    'mouse_id': 9999,  # this mouse doesn't exist!\n",
-    "    'session_date': '2017-05-15',\n",
-    "    'experiment_setup': 0,\n",
-    "    'experimenter': 'Edgar Y. Walker'\n",
+    "    \"mouse_id\": 9999,  # this mouse doesn't exist!\n",
+    "    \"session_date\": \"2017-05-15\",\n",
+    "    \"experiment_setup\": 0,\n",
+    "    \"experimenter\": \"Edgar Y. Walker\",\n",
     "}"
    ]
   },
@@ -1709,7 +1703,7 @@
     }
    ],
    "source": [
-    "Mouse & 'mouse_id = 0'"
+    "Mouse & \"mouse_id = 0\""
    ]
   },
   {
@@ -2886,7 +2880,7 @@
     }
    ],
    "source": [
-    "female_mice & 'mouse_id > 10'"
+    "female_mice & \"mouse_id > 10\""
    ]
   },
   {
@@ -3006,7 +3000,7 @@
     }
    ],
    "source": [
-    "Mouse & Session "
+    "Mouse & Session"
    ]
   },
   {
@@ -3999,7 +3993,7 @@
     }
    ],
    "source": [
-    "Mouse.proj('sex')"
+    "Mouse.proj(\"sex\")"
    ]
   },
   {
@@ -4129,7 +4123,7 @@
     }
    ],
    "source": [
-    "Mouse.proj(date_of_birth='dob')"
+    "Mouse.proj(date_of_birth=\"dob\")"
    ]
   },
   {
@@ -4239,7 +4233,7 @@
     }
    ],
    "source": [
-    "(Mouse * Session).proj(age='datediff(session_date, dob)')"
+    "(Mouse * Session).proj(age=\"datediff(session_date, dob)\")"
    ]
   },
   {
@@ -4379,7 +4373,7 @@
     }
    ],
    "source": [
-    "(Mouse * Session).proj(..., age='datediff(session_date, dob)')"
+    "(Mouse * Session).proj(..., age=\"datediff(session_date, dob)\")"
    ]
   },
   {
@@ -4690,7 +4684,7 @@
     }
    ],
    "source": [
-    "(Mouse & 'sex = \"M\"').fetch(format='frame')"
+    "(Mouse & 'sex = \"M\"').fetch(format=\"frame\")"
    ]
   },
   {
@@ -4717,7 +4711,7 @@
     }
    ],
    "source": [
-    "(Mouse & 'sex = \"M\"').fetch('KEY')"
+    "(Mouse & 'sex = \"M\"').fetch(\"KEY\")"
    ]
   },
   {
@@ -4733,7 +4727,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sex, dob = Mouse.fetch('sex', 'dob')"
+    "sex, dob = Mouse.fetch(\"sex\", \"dob\")"
    ]
   },
   {
@@ -4818,7 +4812,7 @@
     }
    ],
    "source": [
-    "info = Mouse.fetch('sex', 'dob', as_dict=True)\n",
+    "info = Mouse.fetch(\"sex\", \"dob\", as_dict=True)\n",
     "info"
    ]
   },
@@ -4853,7 +4847,9 @@
     }
    ],
    "source": [
-    "mouse_0 = (Mouse & {'mouse_id': 0}).fetch1()  # \"fetch1()\" because we know there's only one\n",
+    "mouse_0 = (\n",
+    "    Mouse & {\"mouse_id\": 0}\n",
+    ").fetch1()  # \"fetch1()\" because we know there's only one\n",
     "mouse_0"
    ]
   },
@@ -4881,7 +4877,7 @@
     }
    ],
    "source": [
-    "(Mouse & {'mouse_id': 0}).fetch1('KEY')"
+    "(Mouse & {\"mouse_id\": 0}).fetch1(\"KEY\")"
    ]
   },
   {
@@ -4897,7 +4893,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sex, dob = (Mouse & {'mouse_id': 0}).fetch1('sex', 'dob')"
+    "sex, dob = (Mouse & {\"mouse_id\": 0}).fetch1(\"sex\", \"dob\")"
    ]
   },
   {
@@ -4978,7 +4974,7 @@
     }
    ],
    "source": [
-    "(Mouse & 'mouse_id = 100').delete()"
+    "(Mouse & \"mouse_id = 100\").delete()"
    ]
   },
   {