meta-edc 1.1.4__tar.gz → 1.1.5__tar.gz

{meta_edc-1.1.4 → meta_edc-1.1.5}/.pre-commit-config.yaml

@@ -3,7 +3,7 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.8.3
+    rev: 1.8.6
     hooks:
       - id: bandit
         args:
@@ -16,7 +16,7 @@ repos:
         language_version: python3.12
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.2
+    rev: 7.3.0
     hooks:
       - id: flake8
         args:
@@ -47,12 +47,12 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/rstcheck/rstcheck
-    rev: v6.2.4
+    rev: v6.2.5
     hooks:
       - id: rstcheck
 
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
+    rev: v1.37.1
     hooks:
       - id: yamllint
         args:

{meta_edc-1.1.4 → meta_edc-1.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: meta-edc
-Version: 1.1.4
+Version: 1.1.5
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -694,7 +694,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.rst
-Requires-Dist: edc==1.1.3
+Requires-Dist: edc==1.1.4
 Requires-Dist: beautifulsoup4
 Requires-Dist: celery[redis]
 Requires-Dist: django-pylabels

{meta_edc-1.1.4 → meta_edc-1.1.5}/meta_analytics/notebooks/pharmacy.ipynb

@@ -21,10 +21,16 @@
     "plus = activate(dotenv_file=env_file)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -70,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -112,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -122,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +171,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -175,7 +181,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +204,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -212,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +241,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -252,7 +258,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,7 +268,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -299,7 +305,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -309,7 +315,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -321,7 +327,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -353,7 +359,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -374,7 +380,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -385,7 +391,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -395,7 +401,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -408,7 +414,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -426,7 +432,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -447,7 +453,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -463,12 +469,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
     "# now lets look at the stock\n",
-    "df_stock = read_frame(Stock.objects.values(\"code\", \"lot_id\", \"container__name\", \"confirmed\", \"allocated\", \"dispensed\", \"qty_in\", \"qty_out\", \"unit_qty_in\", \"unit_qty_out\").all(), verbose=False)\n",
+    "df_stock = read_frame(Stock.objects.values(\"code\", \"lot_id\", \"container__name\", \"confirmation\", \"allocation\", \"dispense\", \"qty_in\", \"qty_out\", \"unit_qty_in\", \"unit_qty_out\").all(), verbose=False)\n",
+    "df_stock = df_stock.fillna(pd.NA)\n",
     "\n",
     "# merge in assignment\n",
     "df_lot = read_frame(Lot.objects.values(\"id\", \"assignment__name\").all(), verbose=False)\n",
@@ -481,7 +488,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -498,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -511,7 +518,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -533,7 +540,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -548,7 +555,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -563,7 +570,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -575,7 +582,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -587,7 +594,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -598,7 +605,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -609,7 +616,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "35",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -620,18 +627,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
     "# tablets: total bottles available / not yet dispensed BY ASSIGNMENT\n",
     "# the total matches the total above for column \"bal\"\n",
-    "df4 = df_stock[(df_stock.container_type==\"Bottle\") & (df_stock.confirmed==True) & (df_stock.dispensed==True)].groupby(by=[\"assignment\"]).unit_qty_in.sum().reset_index()\n",
+    "df4 = df_stock[(df_stock.container_type==\"Bottle\") & ~(df_stock.confirmation.isna()) & ~(df_stock.dispense.isna())].groupby(by=[\"assignment\"]).unit_qty_in.sum().reset_index()\n",
     "df4[\"subtotal\"] = np.nan\n",
     "df4.loc[len(df4)] = {\"subtotal\": df4.unit_qty_in.sum()}\n",
-    "df4[\"dispensed\"] = True\n",
+    "df[\"dispensed\"] = True\n",
     "\n",
-    "df5 = df_stock[(df_stock.container_type==\"Bottle\") & (df_stock.confirmed==True) & (df_stock.dispensed==False)].groupby(by=[\"assignment\"]).unit_qty_in.sum().reset_index()\n",
+    "df5 = df_stock[(df_stock.container_type==\"Bottle\") & ~(df_stock.confirmation.isna()) & (df_stock.dispense.isna())].groupby(by=[\"assignment\"]).unit_qty_in.sum().reset_index()\n",
     "df5.loc[df5.assignment==\"placebo\", \"unit_qty_in\"] +=  placebo_unlabelled\n",
     "df5.loc[df5.assignment==\"active\", \"unit_qty_in\"] +=  active_unlabelled\n",
     "df5[\"subtotal\"] = np.nan\n",
@@ -646,14 +653,6 @@
     "df6"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "36",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -668,14 +667,6 @@
    "id": "38",
    "metadata": {},
    "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "39",
-   "metadata": {},
-   "outputs": [],
    "source": [
     "from meta_visit_schedule.constants import MONTH36\n",
     "\n",
@@ -685,7 +676,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "39",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -724,7 +715,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "41",
+   "id": "40",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -744,7 +735,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "41",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -755,7 +746,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43",
+   "id": "42",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -766,7 +757,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44",
+   "id": "43",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -774,7 +765,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45",
+   "id": "44",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -800,7 +791,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "45",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -810,7 +801,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47",
+   "id": "46",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -833,7 +824,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48",
+   "id": "47",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -843,7 +834,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "49",
+   "id": "48",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -859,7 +850,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "50",
+   "id": "49",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -870,7 +861,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "51",
+   "id": "50",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -890,7 +881,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52",
+   "id": "51",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -898,7 +889,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "53",
+   "id": "52",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -906,7 +897,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "54",
+   "id": "53",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -916,7 +907,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "55",
+   "id": "54",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -926,7 +917,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "56",
+   "id": "55",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -937,7 +928,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "57",
+   "id": "56",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -950,7 +941,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "58",
+   "id": "57",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -962,7 +953,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "59",
+   "id": "58",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -972,7 +963,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "60",
+   "id": "59",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -983,7 +974,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "61",
+   "id": "60",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -995,7 +986,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "62",
+   "id": "61",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1008,7 +999,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "63",
+   "id": "62",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1022,7 +1013,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "64",
+   "id": "63",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1032,7 +1023,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "65",
+   "id": "64",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -1040,7 +1031,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "66",
+   "id": "65",
    "metadata": {},
    "outputs": [],
    "source": []