black formatting

Author: MilagrosMarin

.github/workflows/codespell.yml

@@ -1,4 +1,3 @@
----
 name: Codespell
 
 on:

completed_tutorials/03-Calcium Imaging Computed Tables.ipynb

@@ -1416,7 +1416,6 @@
     "    def make(\n",
     "        self, key\n",
     "    ):  # key is one of the primary keys of the join product of AverageFrame and ParameterSet\n",
-    "\n",
     "        print(\"Populating for: \", key)\n",
     "\n",
     "        # fetch average image from the previous table AverageFrame\n",
@@ -2738,7 +2737,6 @@
     "\n",
     "    # the master table is mainly to perform the computation, while the part table contains the result\n",
     "    def make(self, key):\n",
-    "\n",
     "        print(\"Populating: {}\".format(key))\n",
     "        # fetch data directory from table Session\n",
     "        data_path = \"../01-Calcium_Imaging/\" + (Session & key).fetch1(\"data_path\")\n",
@@ -2764,7 +2762,6 @@
     "\n",
     "        traces = []\n",
     "        for roi_key, mask in zip(roi_keys, masks):\n",
-    "\n",
     "            # reshape mask\n",
     "            mask_reshaped = np.reshape(mask, [w * h])\n",
     "            trace = np.mean(im_reshaped[:, mask_reshaped], axis=1)\n",

completed_tutorials/05-Electrophysiology Computed Tables.ipynb

@@ -2223,7 +2223,6 @@
     "            40,\n",
     "        )  # extract 40 sample points before and after a spike as the waveform\n",
     "        for spk_id, spk in enumerate(np.where(spikes == 1)[0]):\n",
-    "\n",
     "            # For simplicity, skip the spikes too close to the beginning or the end\n",
     "            if spk - before_spk < 0 or spk + after_spk > len(activity) + 1:\n",
     "                continue\n",

db-course/006-Joins-HW.ipynb

@@ -1895,7 +1895,7 @@
     }
    ],
    "source": [
-    "dj.Diagram (nations)"
+    "dj.Diagram(nations)"
    ]
   },
   {

db-course/008-Transactions.ipynb

@@ -249,7 +249,6 @@
    "outputs": [],
    "source": [
     "def transfer_bad(account1, account2, amount):\n",
-    "\n",
     "    current_balance = (Account & account1).fetch1(\"balance\")\n",
     "    if current_balance < amount:\n",
     "        raise RuntimeError(\"Insufficient funds\")\n",
@@ -268,10 +267,8 @@
    "outputs": [],
    "source": [
     "def transfer_good(account1, account2, amount):\n",
-    "\n",
     "    conn = dj.conn()\n",
     "    with conn.transaction:\n",
-    "\n",
     "        current_balance = (Account & account1).fetch1(\"balance\")\n",
     "        if current_balance < amount:\n",
     "            raise RuntimeError(\"Insufficient funds\")\n",
@@ -634,7 +631,6 @@
    "outputs": [],
    "source": [
     "def transfer(cursor, account1, account2, amount):\n",
-    "\n",
     "    cursor.execute(\"BEGIN TRANSACTION\")\n",
     "\n",
     "    try:\n",

db-course/DesignPatterns.ipynb

@@ -287,9 +287,7 @@
    "outputs": [],
    "source": [
     "def transfer(account1, account2, amount):\n",
-    "\n",
     "    with Account.connection.transaction:\n",
-    "\n",
     "        current_balance = (Account & account1).fetch1(\"balance\")\n",
     "        if current_balance < amount:\n",
     "            raise RuntimeError(\"Insufficient funds\")\n",
@@ -1359,7 +1357,6 @@
    "outputs": [],
    "source": [
     "def transfer(cursor, account1, account2, amount):\n",
-    "\n",
     "    cursor.execute(\"BEGIN TRANSACTION\")\n",
     "\n",
     "    try:\n",

tutorials/03-Calcium Imaging Computed Tables.ipynb

@@ -537,7 +537,6 @@
     "    def make(\n",
     "        self, key\n",
     "    ):  # key is one of the primary keys of the join product of AverageFrame and ParameterSet\n",
-    "\n",
     "        print(\"Populating for: \", key)\n",
     "\n",
     "        # fetch average image from the previous table AverageFrame\n",
@@ -912,7 +911,6 @@
     "\n",
     "    # the master table is mainly to perform the computation, while the part table contains the result\n",
     "    def make(self, key):\n",
-    "\n",
     "        print(\"Populating: {}\".format(key))\n",
     "        # fetch data directory from table Session\n",
     "        data_path = (Session & key).fetch1(\"data_path\")\n",
@@ -938,7 +936,6 @@
     "\n",
     "        traces = []\n",
     "        for roi_key, mask in zip(roi_keys, masks):\n",
-    "\n",
     "            # reshape mask\n",
     "            mask_reshaped = np.reshape(mask, [w * h])\n",
     "            trace = np.mean(im_reshaped[:, mask_reshaped], axis=1)\n",

tutorials/05-Electrophysiology Computed Tables.ipynb

@@ -777,7 +777,6 @@
     "            40,\n",
     "        )  # extract 40 sample points before and after a spike as the waveform\n",
     "        for spk_id, spk in enumerate(np.where(spikes == 1)[0]):\n",
-    "\n",
     "            # For simplicity, skip the spikes too close to the beginning or the end\n",
     "            if spk - before_spk < 0 or spk + after_spk > len(activity) + 1:\n",
     "                continue\n",