some ignore changes and test workflow

.github/workflows/test.yml

@@ -0,0 +1,25 @@
+name: Test CI
+on: push
+
+jobs:
+  ci:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+        poetry-version: ["1.0", "1.1.15"]
+        os: [ubuntu-18.04, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Run image
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Install Requirements
+        run: poetry install
+      - name: Test Phenotron
+        run: poetry run pytest

.gitignore

@@ -131,3 +131,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Phenopackets
+phenopackets/

notebooks/PRENATALSEQ.ipynb

@@ -0,0 +1,133 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "cd9d0c49",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import phenopackets as pp\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "pd.set_option('display.max_colwidth', None)\n",
+    "from pyphetools.creation import *\n",
+    "import logging\n",
+    "\n",
+    "def done():\n",
+    "    logging.info(\"Done..\")\n",
+    "    \n",
+    "from hpotk import Ontology\n",
+    "from hpotk.ontology.load.obographs import load_ontology\n",
+    "\n",
+    "logging.info(\"Loading graph data..\")\n",
+    "o: Ontology = load_ontology('http://purl.obolibrary.org/obo/hp.json')\n",
+    "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\")\n",
+    "metadata.default_versions_with_hpo(version=o.version)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "7faffa97",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "logging.info('Loading neonatal data [{0}].'.format(\"/Users/gargam/Develop/neonatal-packets/examples/pexample.csv\"))\n",
+    "df = pd.read_csv(\"/Users/gargam/Develop/neonatal-packets/examples/pexample.csv\", sep=\"\\t\", keep_default_na=False)\n",
+    "done()\n",
+    "logging.info(\"Identifying hpo columns..\")\n",
+    "logging.info(\"Scanning samples that have no phenotypes..\")\n",
+    "phenotype_col = \"Anomalies with HPO codes (Screening)\"\n",
+    "empty_idx = np.where(df[phenotype_col].eq('') | df[phenotype_col].isna())[0].tolist()\n",
+    "empty_samples = [df.iloc[i, 0] for i in empty_idx]\n",
+    "logging.info(empty_samples)\n",
+    "\n",
+    "logging.info(\"Dropping empties..\")\n",
+    "df.drop(empty_idx, axis=0, inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "2556e305",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def to_hpterm(terms, o):\n",
+    "    result = []\n",
+    "    for term in terms:\n",
+    "        term = o.get_term(term.replace(' ', ''))\n",
+    "        if term == None:\n",
+    "            print(terms)\n",
+    "        result.append(HpTerm(term.identifier.value, term.name))\n",
+    "    return result"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "6dc21c62",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "logging.info(\"Mapping rows to phenopackets...\")\n",
+    "samples = []\n",
+    "for index, row in df.iterrows():\n",
+    "    terms = to_hpterm(row[2].split(\",\"), o)\n",
+    "    samples.append(Individual(row[0], terms, interpretation_list=[]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "265e53f5",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "101"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "Individual.output_individuals_as_phenopackets(samples, metadata = metadata.to_ga4gh())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2265503b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "updated",
+   "language": "python",
+   "name": "updated"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}