Test on Apple silicon (#710)

* Test on Apple silicon * psycopg2 * install conda * lint
open-reaction-database · Feb 13, 2024 · 0827264 · 0827264
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diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -18,12 +18,17 @@ on: [ pull_request, push ]
 
 jobs:
   test_ord_schema:
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
+    runs-on: ${{ matrix.os }}
     env:
       PGDATA: $GITHUB_WORKSPACE/rdkit-postgres
     steps:
       - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: 'latest'
       - name: Setup PostgreSQL
         shell: bash -l {0}
         run: |
@@ -47,7 +52,10 @@ jobs:
       - uses: codecov/codecov-action@v1
 
   test_notebooks:
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-14 ]
+    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4

diff --git a/examples/submissions/3_Liu_Copper_OrgSyn/example_liu.ipynb b/examples/submissions/3_Liu_Copper_OrgSyn/example_liu.ipynb
@@ -831,9 +831,9 @@
     "\n",
     "outcome.analyses[\"quantitative NMR\"].type = analysis.NMR_1H\n",
     "outcome.analyses[\"quantitative NMR\"].is_of_isolated_species = True\n",
-    "outcome.analyses[\n",
-    "    \"quantitative NMR\"\n",
-    "].details = \"Quantitative NMR using 1,1,2,2-tetrachloroethane (>98%, purchased from Alfa Aesar) in CDCl3\"\n",
+    "outcome.analyses[\"quantitative NMR\"].details = (\n",
+    "    \"Quantitative NMR using 1,1,2,2-tetrachloroethane (>98%, purchased from Alfa Aesar) in CDCl3\"\n",
+    ")\n",
     "\n",
     "# A single product was desired and characterized\n",
     "product = outcome.products.add()\n",
@@ -1739,15 +1739,15 @@
     "\n",
     "outcome.analyses[\"quantitative NMR\"].type = analysis.NMR_1H\n",
     "outcome.analyses[\"quantitative NMR\"].is_of_isolated_species = True\n",
-    "outcome.analyses[\n",
-    "    \"quantitative NMR\"\n",
-    "].details = \"Quantitative NMR using ferrocene (98%, purchased from Sigma-Aldrich, recrystallized from pentane) in CDCl3\"\n",
+    "outcome.analyses[\"quantitative NMR\"].details = (\n",
+    "    \"Quantitative NMR using ferrocene (98%, purchased from Sigma-Aldrich, recrystallized from pentane) in CDCl3\"\n",
+    ")\n",
     "\n",
     "outcome.analyses[\"chiral HPLC\"].type = analysis.LC\n",
     "outcome.analyses[\"chiral HPLC\"].is_of_isolated_species = True\n",
-    "outcome.analyses[\n",
-    "    \"chiral HPLC\"\n",
-    "].details = \"HPLC (Daicel Chiralpak OD-H column), eluting with 4% isopropanol in hexanes at 0.6 mL/min: 10.9 min (minor), 13.4 min (major), 98% ee for the first run and 99% ee for the second run\"\n",
+    "outcome.analyses[\"chiral HPLC\"].details = (\n",
+    "    \"HPLC (Daicel Chiralpak OD-H column), eluting with 4% isopropanol in hexanes at 0.6 mL/min: 10.9 min (minor), 13.4 min (major), 98% ee for the first run and 99% ee for the second run\"\n",
+    ")\n",
     "\n",
     "outcome.analyses[\"specific rotation\"].type = analysis.CD\n",
     "outcome.analyses[\"specific rotation\"].is_of_isolated_species = True\n",
@@ -2671,15 +2671,15 @@
     "\n",
     "outcome.analyses[\"quantitative NMR\"].type = analysis.NMR_1H\n",
     "outcome.analyses[\"quantitative NMR\"].is_of_isolated_species = True\n",
-    "outcome.analyses[\n",
-    "    \"quantitative NMR\"\n",
-    "].details = \"Quantitative NMR using ferrocene (98%, purchased from Sigma-Aldrich, recrystallized from pentane) in CDCl3\"\n",
+    "outcome.analyses[\"quantitative NMR\"].details = (\n",
+    "    \"Quantitative NMR using ferrocene (98%, purchased from Sigma-Aldrich, recrystallized from pentane) in CDCl3\"\n",
+    ")\n",
     "\n",
     "outcome.analyses[\"chiral SFC\"].type = analysis.SFC\n",
     "outcome.analyses[\"chiral SFC\"].is_of_isolated_species = True\n",
-    "outcome.analyses[\n",
-    "    \"chiral SFC\"\n",
-    "].details = \"FC (Daicel Chiralpak AD-H column, heated to 40 °C), eluting with a linear gradient over 6 min from 5% to 10% isopropanol in supercritical CO2 at 2.5 mL/min.: 2.57 min (major), 2.98 min (minor), 90% ee for both runs\"\n",
+    "outcome.analyses[\"chiral SFC\"].details = (\n",
+    "    \"FC (Daicel Chiralpak AD-H column, heated to 40 °C), eluting with a linear gradient over 6 min from 5% to 10% isopropanol in supercritical CO2 at 2.5 mL/min.: 2.57 min (major), 2.98 min (minor), 90% ee for both runs\"\n",
+    ")\n",
     "\n",
     "outcome.analyses[\"specific rotation\"].type = analysis.CD\n",
     "outcome.analyses[\"specific rotation\"].is_of_isolated_species = True\n",

diff --git a/examples/submissions/9_Ahneman_Science_CN_Coupling/example_Ahenman.ipynb b/examples/submissions/9_Ahneman_Science_CN_Coupling/example_Ahenman.ipynb
@@ -333,9 +333,9 @@
     "# Analyses: UPLC\n",
     "# Note using LCMS because UPLC is not an option\n",
     "outcome.analyses[\"UPLC analysis\"].type = reaction_pb2.Analysis.LCMS\n",
-    "outcome.analyses[\n",
-    "    \"UPLC analysis\"\n",
-    "].details = \"UPLC using 3 µL of 0.0025 M di-tert-butylbiphenyl solution in DMSO external standard\"\n",
+    "outcome.analyses[\"UPLC analysis\"].details = (\n",
+    "    \"UPLC using 3 µL of 0.0025 M di-tert-butylbiphenyl solution in DMSO external standard\"\n",
+    ")\n",
     "outcome.analyses[\"UPLC analysis\"].instrument_manufacturer = \"Waters Acquity\"\n",
     "\n",
     "# Define product identity\n",
@@ -1586,9 +1586,9 @@
     "\n",
     "    # Analyses: UPLC/MS\n",
     "    outcome.analyses[\"UPLC analysis\"].type = reaction_pb2.Analysis.LCMS\n",
-    "    outcome.analyses[\n",
-    "        \"UPLC analysis\"\n",
-    "    ].details = \"UPLC using 3 µL of 0.0025 M di-tert-butylbiphenyl solution in DMSO external standard\"\n",
+    "    outcome.analyses[\"UPLC analysis\"].details = (\n",
+    "        \"UPLC using 3 µL of 0.0025 M di-tert-butylbiphenyl solution in DMSO external standard\"\n",
+    "    )\n",
     "    outcome.analyses[\"UPLC analysis\"].instrument_manufacturer = \"Waters Acquity\"\n",
     "\n",
     "    # Define product identity\n",

diff --git a/ord_schema/orm/database.py b/ord_schema/orm/database.py
@@ -35,7 +35,7 @@ def get_connection_string(
     database: str, username: str, password: str, host: str = "localhost", port: int = 5432
 ) -> str:
     """Creates an SQLAlchemy connection string."""
-    return f"postgresql://{username}:{password}@{host}:{port}/{database}"
+    return f"postgresql://{username}:{password}@{host}:{port}/{database}?client_encoding=utf-8"
 
 
 def prepare_database(engine: Engine) -> bool:

diff --git a/setup.py b/setup.py
@@ -43,7 +43,7 @@
         "openpyxl>=3.0.5",
         "pandas>=1.0.4",
         "protobuf==4.22.3",
-        "psycopg2>=2.8.5",
+        "psycopg2-binary>=2.8.5",
         "pygithub>=1.51",
         "python-dateutil>=1.10.0",
         "rdkit>=2021.9.5",