Merge pull request #4 from SalvadorBrandolin/use_path_lib_models

pathlib to models module and windows and Mac to CI

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
   - workflow_dispatch
 
 jobs:
-  test:
+  test-linux:
 
     runs-on: ubuntu-latest
     strategy:
@@ -26,3 +26,44 @@ jobs:
         run: pip install tox tox-gh-actions
       - name: Test with tox
         run: tox -r
+
+  test-windows:
+
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version}}
+          architecture: x64
+      - name: Install pandoc
+        run: choco install pandoc
+      - name: Install tox
+        run: pip install tox tox-gh-actions
+      - name: Test with tox
+        run: tox -r
+
+  test-macos:
+
+    runs-on: macOS-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version}}
+      - name: Install pandoc
+        run: brew install pandoc
+      - name: Install tox
+        run: pip install tox tox-gh-actions
+      - name: Test with tox
+        run: tox -r

tests/writers/test_to_clapeyron.py

@@ -10,18 +10,18 @@
 from ugropy.writers.clapeyron_writers import write_molar_mass
 
 
-here = Path(__file__).parent.resolve()
-path_db = f"{here}/test_expected_result"
+here = Path(__file__).parent
+path_db = here / "test_expected_result"
 
 
 def test_to_clapeyron():
-    with open(f"{path_db}/molarmass.csv", mode="r") as f:
+    with open(path_db / "molarmass.csv", mode="r") as f:
         df_molarmass = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{path_db}/ogUNIFAC_groups.csv", mode="r") as f:
+    with open(path_db / "ogUNIFAC_groups.csv", mode="r") as f:
         df_unifac = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{path_db}/PSRK_groups.csv", mode="r") as f:
+    with open(path_db / "PSRK_groups.csv", mode="r") as f:
         df_psrk = pd.read_csv(f, sep="|", index_col=None)
 
     limonene = Groups("CC1=CCC(CC1)C(=C)C", "smiles")
@@ -32,19 +32,21 @@ def test_to_clapeyron():
         [limonene.unifac.subgroups, ethanol.unifac.subgroups],
         [limonene.psrk.subgroups, ethanol.psrk.subgroups],
         [limonene.joback, ethanol.joback],
-        f"{here}/database",
+        (here / "database").resolve(),
     )
 
-    with open(f"{here}/database/critical.csv", mode="r") as f:
+    with open(here / "database" / "critical.csv", mode="r") as f:
         df_critical_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{here}/database/molarmass.csv", mode="r") as f:
+    with open(here / "database" / "molarmass.csv", mode="r") as f:
         df_molarmass_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{here}/database/ogUNIFAC/ogUNIFAC_groups.csv", mode="r") as f:
+    with open(
+        here / "database" / "ogUNIFAC" / "ogUNIFAC_groups.csv", mode="r"
+    ) as f:
         df_unifac_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{here}/database/PSRK/PSRK_groups.csv", mode="r") as f:
+    with open(here / "database" / "PSRK/PSRK_groups.csv", mode="r") as f:
         df_psrk_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
     assert df_unifac.equals(df_unifac_ugropy)
@@ -72,23 +74,23 @@ def test_to_clapeyron():
         == "ethanol,,519.5440517502864,5756641.437226128,0.00016649999999999998,0.5610678012451401"  # noqa
     )
 
-    os.remove(f"{here}/database/critical.csv")
-    os.remove(f"{here}/database/molarmass.csv")
-    os.remove(f"{here}/database/ogUNIFAC/ogUNIFAC_groups.csv")
-    os.remove(f"{here}/database/PSRK/PSRK_groups.csv")
-    os.rmdir(f"{here}/database/ogUNIFAC")
-    os.rmdir(f"{here}/database/PSRK")
-    os.rmdir(f"{here}/database")
+    os.remove(here / "database" / "critical.csv")
+    os.remove(here / "database" / "molarmass.csv")
+    os.remove(here / "database" / "ogUNIFAC" / "ogUNIFAC_groups.csv")
+    os.remove(here / "database" / "PSRK" / "PSRK_groups.csv")
+    os.rmdir(here / "database" / "ogUNIFAC")
+    os.rmdir(here / "database/PSRK")
+    os.rmdir(here / "database")
 
 
 def test_to_clapeyron_batch_name():
-    with open(f"{path_db}/molarmass.csv", mode="r") as f:
+    with open(path_db / "molarmass.csv", mode="r") as f:
         df_molarmass = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{path_db}/ogUNIFAC_groups.csv", mode="r") as f:
+    with open(path_db / "ogUNIFAC_groups.csv", mode="r") as f:
         df_unifac = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{path_db}/PSRK_groups.csv", mode="r") as f:
+    with open(path_db / "PSRK_groups.csv", mode="r") as f:
         df_psrk = pd.read_csv(f, sep="|", index_col=None)
 
     limonene = Groups("CC1=CCC(CC1)C(=C)C", "smiles")
@@ -99,22 +101,24 @@ def test_to_clapeyron_batch_name():
         [limonene.unifac.subgroups, ethanol.unifac.subgroups],
         [limonene.psrk.subgroups, ethanol.psrk.subgroups],
         [limonene.joback, ethanol.joback],
-        f"{here}/database",
+        (here / "database").resolve(),
         "otacon",
     )
 
-    with open(f"{here}/database/otacon_critical.csv", mode="r") as f:
+    with open(here / "database" / "otacon_critical.csv", mode="r") as f:
         df_critical_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{here}/database/otacon_molarmass.csv", mode="r") as f:
+    with open(here / "database" / "otacon_molarmass.csv", mode="r") as f:
         df_molarmass_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
     with open(
-        f"{here}/database/ogUNIFAC/otacon_ogUNIFAC_groups.csv", mode="r"
+        here / "database" / "ogUNIFAC" / "otacon_ogUNIFAC_groups.csv", mode="r"
     ) as f:
         df_unifac_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
-    with open(f"{here}/database/PSRK/otacon_PSRK_groups.csv", mode="r") as f:
+    with open(
+        here / "database" / "PSRK" / "otacon_PSRK_groups.csv", mode="r"
+    ) as f:
         df_psrk_ugropy = pd.read_csv(f, sep="|", index_col=None)
 
     assert df_unifac.equals(df_unifac_ugropy)
@@ -142,13 +146,13 @@ def test_to_clapeyron_batch_name():
         == "ethanol,,519.5440517502864,5756641.437226128,0.00016649999999999998,0.5610678012451401"  # noqa
     )
 
-    os.remove(f"{here}/database/otacon_critical.csv")
-    os.remove(f"{here}/database/otacon_molarmass.csv")
-    os.remove(f"{here}/database/ogUNIFAC/otacon_ogUNIFAC_groups.csv")
-    os.remove(f"{here}/database/PSRK/otacon_PSRK_groups.csv")
-    os.rmdir(f"{here}/database/ogUNIFAC")
-    os.rmdir(f"{here}/database/PSRK")
-    os.rmdir(f"{here}/database")
+    os.remove(here / "database" / "otacon_critical.csv")
+    os.remove(here / "database" / "otacon_molarmass.csv")
+    os.remove(here / "database" / "ogUNIFAC" / "otacon_ogUNIFAC_groups.csv")
+    os.remove(here / "database" / "PSRK" / "otacon_PSRK_groups.csv")
+    os.rmdir(here / "database" / "ogUNIFAC")
+    os.rmdir(here / "database" / "PSRK")
+    os.rmdir(here / "database")
 
 
 def test_molar_mass_csv():
@@ -161,22 +165,22 @@ def test_molar_mass_csv():
         ["limonene", "ethanol"],
         unifac_groups=[limonene.unifac.subgroups, ethanol.unifac.subgroups],
         psrk_groups=[limonene.psrk.subgroups, ethanol.psrk.subgroups],
-        path=f"{here}/database",
+        path=(here / "database").resolve(),
     )
 
-    with open(f"{here}/database/molarmass.csv", mode="r") as f:
+    with open(here / "database" / "molarmass.csv", mode="r") as f:
         df_molarmass_unifac = pd.read_csv(f, sep="|", index_col=None)
 
-    os.remove(f"{here}/database/molarmass.csv")
+    os.remove(here / "database" / "molarmass.csv")
 
     # PSRK molar mass
     to_clapeyron(
         ["limonene", "ethanol"],
         psrk_groups=[limonene.psrk.subgroups, ethanol.psrk.subgroups],
-        path=f"{here}/database",
+        path=(here / "database").resolve(),
     )
 
-    with open(f"{here}/database/molarmass.csv", mode="r") as f:
+    with open(here / "database" / "molarmass.csv", mode="r") as f:
         df_molarmass_psrk = pd.read_csv(f, sep="|", index_col=None)
 
     assert (
@@ -192,17 +196,17 @@ def test_molar_mass_csv():
     assert df_molarmass_unifac.iloc[3].to_numpy()[0] == "ethanol,,46.069"
     assert df_molarmass_unifac.equals(df_molarmass_psrk)
 
-    os.remove(f"{here}/database/molarmass.csv")
-    os.remove(f"{here}/database/ogUNIFAC/ogUNIFAC_groups.csv")
-    os.remove(f"{here}/database/PSRK/PSRK_groups.csv")
-    os.rmdir(f"{here}/database/ogUNIFAC")
-    os.rmdir(f"{here}/database/PSRK")
-    os.rmdir(f"{here}/database")
+    os.remove(here / "database" / "molarmass.csv")
+    os.remove(here / "database" / "ogUNIFAC" / "ogUNIFAC_groups.csv")
+    os.remove(here / "database" / "PSRK" / "PSRK_groups.csv")
+    os.rmdir(here / "database" / "ogUNIFAC")
+    os.rmdir(here / "database" / "PSRK")
+    os.rmdir(here / "database")
 
     # Making it fail
     with pytest.raises(ValueError):
         write_molar_mass(
-            path=f"{here}/database",
+            path=(here / "database").resolve(),
             batch_name=None,
             molecules_names=["limonene", "ethanol"],
         )

ugropy/constants.py

@@ -10,10 +10,10 @@
 
 
 # constants.py path
-_here = Path(__file__).parent.resolve()
+_here = Path(__file__).parent
 
 # CSVs path
-_csvs = f"{_here}/groupscsv"
+_csvs = _here / "groupscsv"
 
 # Gas constant [J/mol/K]
 R = 8.31446261815324

ugropy/fragmentation_models/models.py

@@ -22,7 +22,7 @@ def _rd(file_path: str, index_col: str = None) -> pd.DataFrame:
 
     Parameters
     ----------
-    file_path : str
+    file_path : str or pathlib
         Path to csv file.
     index_col : str, optional
         Name of the index column, by default None.
@@ -39,13 +39,13 @@ def _rd(file_path: str, index_col: str = None) -> pd.DataFrame:
 # =============================================================================
 # LV-UNIFAC
 # =============================================================================
-_uni = f"{_csvs}/unifac"
+_uni = _csvs / "unifac"
 
-_uni_sg = _rd(f"{_uni}/unifac_subgroups.csv", "group")
-_uni_mg = _rd(f"{_uni}/unifac_maingroups.csv", "no.")
-_uni_info = _rd(f"{_uni}/unifac_info.csv", "group")
-_uni_problems = _rd(f"{_csvs}/problematic_structures.csv", "smarts")
-_uni_hide = _rd(f"{_uni}/hideouts.csv", "group")
+_uni_sg = _rd(_uni / "unifac_subgroups.csv", "group")
+_uni_mg = _rd(_uni / "unifac_maingroups.csv", "no.")
+_uni_info = _rd(_uni / "unifac_info.csv", "group")
+_uni_problems = _rd(_csvs / "problematic_structures.csv", "smarts")
+_uni_hide = _rd(_uni / "hideouts.csv", "group")
 
 unifac = GibbsModel(
     subgroups=_uni_sg,
@@ -60,13 +60,13 @@ def _rd(file_path: str, index_col: str = None) -> pd.DataFrame:
 # =============================================================================
 # PSRK
 # =============================================================================
-_psrk = f"{_csvs}/psrk"
+_psrk = _csvs / "psrk"
 
-_psrk_sg = _rd(f"{_psrk}/psrk_subgroups.csv", "group")
-_psrk_mg = _rd(f"{_psrk}/psrk_maingroups.csv", "no.")
-_psrk_info = _rd(f"{_psrk}/psrk_info.csv", "group")
-_psrk_problems = _rd(f"{_csvs}/problematic_structures.csv", "smarts")
-_psrk_hide = _rd(f"{_psrk}/hideouts.csv", "group")
+_psrk_sg = _rd(_psrk / "psrk_subgroups.csv", "group")
+_psrk_mg = _rd(_psrk / "psrk_maingroups.csv", "no.")
+_psrk_info = _rd(_psrk / "psrk_info.csv", "group")
+_psrk_problems = _rd(_csvs / "problematic_structures.csv", "smarts")
+_psrk_hide = _rd(_psrk / "hideouts.csv", "group")
 
 psrk = GibbsModel(
     subgroups=_psrk_sg,
@@ -97,11 +97,11 @@ def _rd(file_path: str, index_col: str = None) -> pd.DataFrame:
 # =============================================================================
 # Joback
 # =============================================================================
-_jo = f"{_csvs}/joback"
+_jo = _csvs / "joback"
 
-_jo_sg = _rd(f"{_jo}/joback_subgroups.csv", "group")
-_jo_problems = _rd(f"{_jo}/joback_problematics.csv", "smarts")
-_jo_props = _rd(f"{_jo}/properties_contrib.csv", "group")
+_jo_sg = _rd(_jo / "joback_subgroups.csv", "group")
+_jo_problems = _rd(_jo / "joback_problematics.csv", "smarts")
+_jo_props = _rd(_jo / "properties_contrib.csv", "group")
 
 joback = PropertiesEstimator(
     subgroups=_jo_sg,
@@ -114,12 +114,12 @@ def _rd(file_path: str, index_col: str = None) -> pd.DataFrame:
 # Constantinou and Gani
 # =============================================================================
 # Primary structures
-_cg = f"{_csvs}/constantinou_gani"
+_cg_p = _csvs / "constantinou_gani" / "primary"
 
-_cg_sg = _rd(f"{_cg}/primary/c_g_prymary_subgroups.csv", "group")
-_cg_problems = _rd(f"{_cg}/primary/cg_problematics.csv", "smarts")
-_cg_hide = _rd(f"{_cg}/primary/hideouts.csv", "group")
-_cg_props = _rd(f"{_cg}/primary/properties_prymary_contrib.csv", "group")
+_cg_sg = _rd(_cg_p / "c_g_prymary_subgroups.csv", "group")
+_cg_problems = _rd(_cg_p / "cg_problematics.csv", "smarts")
+_cg_hide = _rd(_cg_p / "hideouts.csv", "group")
+_cg_props = _rd(_cg_p / "properties_prymary_contrib.csv", "group")
 
 constantinou_gani_primary = PropertiesEstimator(
     subgroups=_cg_sg,

ugropy/writers/clapeyron.py

@@ -18,7 +18,7 @@ def to_clapeyron(
     unifac_groups: List[dict] = [],
     psrk_groups: List[dict] = [],
     joback_objects: List[JobackProperties] = [],
-    path: str = "./database",
+    path: str = "database",
     batch_name: str = "",
 ) -> None:
     """Write the .csv input files for Clapeyron.jl.
@@ -51,9 +51,6 @@ def to_clapeyron(
     if len(molecules_names) == 0:
         raise ValueError("No names provided for the molecules.")
 
-    if not path_pathlib.is_dir():
-        path_pathlib.mkdir(parents=True)
-
     if unifac_groups and len(unifac_groups) != len(molecules_names):
         raise ValueError(
             "UNIFAC groups list must have the same amount of elements than"
@@ -72,6 +69,10 @@ def to_clapeyron(
             "the molecules name list."
         )
 
+    # Create dir if not created
+    if not path_pathlib.is_dir():
+        path_pathlib.mkdir(parents=True)
+
     # Molar mass
     write_molar_mass(
         path_pathlib,