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pathlib to models module and Windows and MacOS added to CI #25

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Apr 23, 2024
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pathlib to models module and Windows and MacOS added to CI #25

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30fc00f
pathlib to models module and windows and Mac to CI
SalvadorBrandolin Apr 23, 2024
c217f7a
Merge pull request #4 from SalvadorBrandolin/use_path_lib_models
SalvadorBrandolin Apr 23, 2024
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43 changes: 42 additions & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ on:
- workflow_dispatch

jobs:
test:
test-linux:

runs-on: ubuntu-latest
strategy:
Expand All @@ -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
92 changes: 48 additions & 44 deletions tests/writers/test_to_clapeyron.py
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Expand Up @@ -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")
Expand All @@ -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)
Expand Down Expand Up @@ -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")
Expand All @@ -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)
Expand Down Expand Up @@ -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():
Expand All @@ -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 (
Expand All @@ -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"],
)
Expand Down
4 changes: 2 additions & 2 deletions ugropy/constants.py
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Expand Up @@ -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
44 changes: 22 additions & 22 deletions ugropy/fragmentation_models/models.py
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Expand Up @@ -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.
Expand All @@ -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,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand Down
9 changes: 5 additions & 4 deletions ugropy/writers/clapeyron.py
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Expand Up @@ -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.
Expand Down Expand Up @@ -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"
Expand All @@ -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,
Expand Down
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