From 34036553a2d1db057c28de74867e5f273a8a1033 Mon Sep 17 00:00:00 2001 From: Andrew Date: Mon, 23 Sep 2024 10:58:09 -0400 Subject: [PATCH] Update the Carsus environment (#406) * Updates the Carsus environment and fixes most issues * Removes leftover testing references to SQL and arraydiff * Fix tests requiring astropy parts * Fixes deprecation and possibly astropy units issue * Fixes some deprecations * Workaround for ChiantiPy bug * Another minor formatting issue * Fixes CMFGEN tests * Add comment regarding temperature "fix" for ChiantiPy * Fixes TARDIS data export and hashing using pickle (sadly) * Reverts accidental commit --- .github/workflows/tests.yml | 3 +- carsus/conftest.py | 45 - carsus/data/basic_atomic_data.csv | 2 +- carsus/io/chianti_/chianti_.py | 5 +- carsus/io/cmfgen/base.py | 20 +- carsus/io/kurucz/gfall.py | 4 +- carsus/io/nist/ionization.py | 8 +- carsus/io/output/base.py | 3 +- carsus/io/output/collisions.py | 2 +- carsus/io/output/levels_lines.py | 17 +- carsus/io/output/macro_atom.py | 20 +- carsus/io/output/photo_ionization.py | 4 +- carsus/io/tests/test_cmfgen.py | 1 - carsus/io/tests/test_ionization_grammar.py | 20 +- .../io/tests/test_nist_weightscomp_grammar.py | 26 +- carsus/io/tests/test_util.py | 2 +- carsus/io/zeta.py | 4 +- carsus/util/hash.py | 19 +- carsus/util/helpers.py | 4 +- carsus/util/selected.py | 4 +- carsus/util/tests/test_hash.py | 7 +- carsus/util/tests/test_selected.py | 8 +- carsus_env3.yml | 22 +- conda-linux-64.lock | 502 +- conda-lock.yml | 14733 +++++++++++----- conda-osx-64.lock | 421 +- conda-osx-arm64.lock | 296 + docs/development/testing.rst | 8 - pytest.ini | 1 - 29 files changed, 11413 insertions(+), 4798 deletions(-) create mode 100644 conda-osx-arm64.lock diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 366d1d5ae..0b73eeccc 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -27,8 +27,7 @@ env: CHIANTI_DL_URL: https://download.chiantidatabase.org CHIANTI_DB_VER: CHIANTI_v9.0.1_database.tar.gz PYTEST_FLAGS: --remote-data --refdata=carsus-refdata - --cov=carsus --cov-report=xml --cov-report=html - --arraydiff --arraydiff-reference-path=carsus-refdata/arraydiff + --cov=carsus --cov-report=xml --cov-report=html NBCONVERT_CMD: jupyter nbconvert --execute --ExecutePreprocessor.timeout=600 --to html CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} CMFGEN_DL_URL: http://kookaburra.phyast.pitt.edu/hillier/cmfgen_files diff --git a/carsus/conftest.py b/carsus/conftest.py index 5c93255cb..621a06c2c 100644 --- a/carsus/conftest.py +++ b/carsus/conftest.py @@ -83,23 +83,9 @@ def pytest_collection_modifyitems(config, items): skip_not_with_refdata = pytest.mark.skip( reason="carsus-refdata folder location not specified" ) - skip_not_with_testdb = pytest.mark.skip( - reason="filename for the testing database not specified" - ) for item in items: if "with_refdata" in item.keywords and not config.getoption("--refdata"): item.add_marker(skip_not_with_refdata) - if "with_test_db" in item.keywords and not config.getoption("--test-db"): - item.add_marker(skip_not_with_testdb) - - -@pytest.fixture(scope="session") -def test_db_fname(request): - test_db_fname = request.config.getoption("--test-db") - if test_db_fname is None: - pytest.skip("--testing database was not specified") - else: - return str(Path(test_db_fname).expanduser().resolve()) @pytest.fixture(scope="session") @@ -129,37 +115,6 @@ def nndc_dirname(): return str(DATA_DIR_PATH / "nndc") # Mn-52, Ni-56 -@pytest.fixture(scope="session") -def test_engine(test_db_url): - return create_engine(test_db_url) - - -@pytest.fixture -def test_session(test_engine, request): - # engine.echo=True - # connect to the database - connection = test_engine.connect() - - # begin a non-ORM transaction - trans = connection.begin() - - # bind an individual Session to the connection - session = Session(bind=connection) - - def fin(): - session.close() - # rollback - everything that happened with the - # Session above (including calls to commit()) - # is rolled back. - trans.rollback() - # return connection to the Engine - connection.close() - - request.addfinalizer(fin) - - return session - - @pytest.fixture(scope="session") def refdata_path(request): refdata_path = request.config.getoption("--refdata") diff --git a/carsus/data/basic_atomic_data.csv b/carsus/data/basic_atomic_data.csv index 6f8214020..827604e4e 100644 --- a/carsus/data/basic_atomic_data.csv +++ b/carsus/data/basic_atomic_data.csv @@ -57,7 +57,7 @@ atomic_number,symbol,name,group,period 56,Ba,Barium,2.0,6 57,La,Lanthanum,-1.0,6 58,Ce,Cerium,-1.0,6 -59,Pr,Praseodymium -1 ,-1.0,6 +59,Pr,Praseodymium,-1.0,6 60,Nd,Neodymium,-1.0,6 61,Pm,Promethium,-1.0,6 62,Sm,Samarium,-1.0,6 diff --git a/carsus/io/chianti_/chianti_.py b/carsus/io/chianti_/chianti_.py index 5d6deebc4..e780ca49e 100644 --- a/carsus/io/chianti_/chianti_.py +++ b/carsus/io/chianti_/chianti_.py @@ -39,7 +39,7 @@ def versionRead(): masterlist_ions = pickle.load(masterlist_ions_file).keys() # Exclude the "d" ions for now masterlist_ions = [_ for _ in masterlist_ions - if re.match("^[a-z]+_\d+$", _)] + if re.match(r"^[a-z]+_\d+$", _)] masterlist_version = versionRead() @@ -109,7 +109,8 @@ class ChiantiIonReader(object): def __init__(self, ion_name): - self.ion = ch.ion(ion_name) + # dummy temperature to avoid bug in ChiantiPy https://github.com/chianti-atomic/ChiantiPy/issues/466 + self.ion = ch.ion(ion_name, temperature=1) self._levels = None self._lines = None self._collisions = None diff --git a/carsus/io/cmfgen/base.py b/carsus/io/cmfgen/base.py index 843877e0b..043a22613 100644 --- a/carsus/io/cmfgen/base.py +++ b/carsus/io/cmfgen/base.py @@ -37,7 +37,7 @@ def load(self, fname): config = { "header": None, "index_col": False, - "sep": "\s+", + "sep": r"\s+", "skiprows": skiprows, "nrows": nrows, "engine": "python", @@ -73,7 +73,7 @@ def load(self, fname): self.base = df self.header = header # Re-calculate Lam(A) values - self.base["Lam(A)"] = self.calc_Lam_A() + self.base["Lam(A)"] = self.calc_Lam_A().value def calc_Lam_A(self): """ @@ -112,7 +112,7 @@ def load(self, fname): config = { "header": None, "index_col": False, - "sep": "\s*\|\s*|-?\s+-?\s*|(?<=[^ED\s])-(?=[^\s])", + "sep": r"\s*\|\s*|-?\s+-?\s*|(?<=[^ED\s])-(?=[^\s])", "skiprows": skiprows, "nrows": nrows, "engine": "python", @@ -177,11 +177,11 @@ class CMFGENCollisionalStrengthsParser(BaseParser): def load(self, fname): header = parse_header(fname) - skiprows, _ = find_row(fname, "ransition\T") + skiprows, _ = find_row(fname, r"ransition\T") config = { "header": None, "index_col": False, - "sep": "\s*-?\s+-?|(?<=[^edED])-|(?<=[FDPS]e)-", + "sep": r"\s*-?\s+-?|(?<=[^edED])-|(?<=[FDPS]e)-", "skiprows": skiprows, "engine": "python", } @@ -194,7 +194,7 @@ def load(self, fname): config["nrows"] = end - config["skiprows"] - 2 try: - _, columns = find_row(fname, "ransition\T") + _, columns = find_row(fname, r"ransition\T") columns = columns.split() # NOTE: Comment next line when trying new regexes @@ -659,9 +659,11 @@ def cross_sections_squeeze( lower_level_label = target.attrs["Configuration name"] cross_section_type = target.attrs["Type of cross-section"] - # Remove the "[J]" term from J-splitted levels labels - ion_levels["label"] = ion_levels["label"].str.rstrip("]") - ion_levels["label"] = ion_levels["label"].str.split("[", expand=True) + if ion_levels["label"].str.contains(r"\[").any(): + # Remove the "[J]" term from J-splitted levels labels + ion_levels["label"] = ion_levels["label"].str.rstrip("]") + # Drop the [J] term completely to avoid shape mismatch. Something to perhaps store in the future + ion_levels["label"] = ion_levels["label"].str.split("[", expand=True)[0] try: match = ion_levels.set_index("label").loc[[lower_level_label]] diff --git a/carsus/io/kurucz/gfall.py b/carsus/io/kurucz/gfall.py index 3f1f9f720..94340d3de 100644 --- a/carsus/io/kurucz/gfall.py +++ b/carsus/io/kurucz/gfall.py @@ -252,8 +252,8 @@ def parse_gfall(self, gfall_raw=None): gfall["label_lower"] = gfall["label_lower"].str.strip() gfall["label_upper"] = gfall["label_upper"].str.strip() - gfall["label_lower"] = gfall["label_lower"].str.replace("\s+", " ") - gfall["label_upper"] = gfall["label_upper"].str.replace("\s+", " ") + gfall["label_lower"] = gfall["label_lower"].str.replace(r"\s+", " ") + gfall["label_upper"] = gfall["label_upper"].str.replace(r"\s+", " ") # Ignore lines with the labels "AVARAGE ENERGIES" and "CONTINUUM" ignored_labels = ["AVERAGE", "ENERGIES", "CONTINUUM"] diff --git a/carsus/io/nist/ionization.py b/carsus/io/nist/ionization.py index 97cac79fc..1a3a4f430 100644 --- a/carsus/io/nist/ionization.py +++ b/carsus/io/nist/ionization.py @@ -227,21 +227,21 @@ def parse_ground_level(row): ) try: - lvl_tokens = level.parseString(ground_level) + lvl_tokens = level.parse_string(ground_level) except ParseException: raise lvl["parity"] = lvl_tokens["parity"] try: - lvl["J"] = lvl_tokens["J"] + lvl["J"] = lvl_tokens["J"][0] except KeyError: pass # To handle cases where the ground level J has not been understood: # Take as assumption J=0 if np.isnan(lvl["J"]): - lvl["J"] = "0" + lvl["J"] = 0 logger.warning( f"Set `J=0` for ground state of species `{convert_atomic_number2symbol(row['atomic_number'])} {row['ion_charge']}`." ) @@ -308,7 +308,7 @@ def get_ground_levels(self): """ levels = self.parser.prepare_ground_levels() levels["g"] = 2 * levels["J"] + 1 - levels["g"] = levels["g"].astype(np.int) + levels["g"] = levels["g"].astype(np.int64) levels["energy"] = 0.0 levels = levels[["g", "energy"]] levels = levels.reset_index() diff --git a/carsus/io/output/base.py b/carsus/io/output/base.py index 906cbac05..21846df66 100644 --- a/carsus/io/output/base.py +++ b/carsus/io/output/base.py @@ -220,7 +220,7 @@ def to_hdf(self, fname): total_checksum = hashlib.md5() for key in f.keys(): # update the total checksum to sign the file - total_checksum.update(serialize_pandas_object(f[key]).to_buffer()) + total_checksum.update(serialize_pandas_object(f[key])) # save individual DataFrame/Series checksum checksum = hash_pandas_object(f[key]) @@ -251,7 +251,6 @@ def to_hdf(self, fname): "astropy", "numpy", "pandas", - "pyarrow", "tables", "ChiantiPy", ] diff --git a/carsus/io/output/collisions.py b/carsus/io/output/collisions.py index fec804fdb..bb24d3694 100644 --- a/carsus/io/output/collisions.py +++ b/carsus/io/output/collisions.py @@ -47,7 +47,7 @@ def prepare_collisions(self): collisions_index + ["g_ratio", "delta_e"] + sorted( - [col for col in self.collisions.columns if re.match("^t\d+$", col)] + [col for col in self.collisions.columns if re.match(r"^t\d+$", col)] ) ) diff --git a/carsus/io/output/levels_lines.py b/carsus/io/output/levels_lines.py index 65d0aaa94..354522291 100644 --- a/carsus/io/output/levels_lines.py +++ b/carsus/io/output/levels_lines.py @@ -110,20 +110,19 @@ def ingest_multiple_sources(self, attribute): """ gfall = getattr(self.gfall_reader, attribute) gfall["ds_id"] = 2 + sources = [gfall] if self.chianti_reader is not None: chianti = getattr(self.chianti_reader, attribute) chianti["ds_id"] = 4 - else: - chianti = pd.DataFrame(columns=gfall.columns) + sources.append(chianti) if self.cmfgen_reader is not None: cmfgen = getattr(self.cmfgen_reader, attribute) cmfgen["ds_id"] = 5 - else: - cmfgen = pd.DataFrame(columns=gfall.columns) + sources.append(cmfgen) - return pd.concat([gfall, chianti, cmfgen], sort=True) + return pd.concat(sources, sort=True) # replace with functools.cached_property with Python > 3.8 @property @@ -148,7 +147,7 @@ def all_levels_data(self): levels = self.ingest_multiple_sources("levels") levels["g"] = 2 * levels["j"] + 1 - levels["g"] = levels["g"].astype(np.int) + levels["g"] = levels["g"].astype(np.int64) levels = levels.drop(columns=["j", "label", "method"]) levels = levels.reset_index() levels = levels.rename(columns={"ion_charge": "ion_number"}) @@ -444,7 +443,7 @@ def create_levels_lines( .values ) - levels["level_number"] = levels["level_number"].astype(np.int) + levels["level_number"] = levels["level_number"].astype(np.int64) levels = levels[ [ @@ -478,7 +477,7 @@ def create_levels_lines( lines["f_ul"] = lines["gf"] / lines["g_u"] # Calculate frequency - lines["nu"] = u.Quantity(lines["wavelength"], "AA").to("Hz", u.spectral()) + lines["nu"] = u.Quantity(lines["wavelength"], "AA").to("Hz", u.spectral()).value # Create Einstein coefficients create_einstein_coeff(lines) @@ -490,7 +489,7 @@ def create_levels_lines( # Create and append artificial levels for fully ionized ions artificial_fully_ionized_levels = create_artificial_fully_ionized(levels) - levels = levels.append(artificial_fully_ionized_levels, ignore_index=True) + levels = pd.concat([levels, artificial_fully_ionized_levels], ignore_index=True) levels = levels.sort_values(["atomic_number", "ion_number", "level_number"]) self.levels = levels diff --git a/carsus/io/output/macro_atom.py b/carsus/io/output/macro_atom.py index 54d2c8bb0..58910e078 100644 --- a/carsus/io/output/macro_atom.py +++ b/carsus/io/output/macro_atom.py @@ -42,13 +42,13 @@ def create_macro_atom(self): macro_atom = list() macro_atom_dtype = [ - ("atomic_number", np.int), - ("ion_number", np.int), - ("source_level_number", np.int), - ("target_level_number", np.int), - ("transition_line_id", np.int), - ("transition_type", np.int), - ("transition_probability", np.float), + ("atomic_number", np.int64), + ("ion_number", np.int64), + ("source_level_number", np.int64), + ("target_level_number", np.int64), + ("transition_line_id", np.int64), + ("transition_type", np.int64), + ("transition_probability", np.float64), ] for line_id, row in lines.iterrows(): @@ -146,15 +146,15 @@ def create_macro_atom_references(self): macro_atom_references["count_down"] = macro_atom_references[ "count_down" - ].astype(np.int) + ].astype(np.int64) macro_atom_references["count_up"] = macro_atom_references["count_up"].astype( - np.int + np.int64 ) macro_atom_references["count_total"] = macro_atom_references[ "count_total" - ].astype(np.int) + ].astype(np.int64) self.macro_atom_references = macro_atom_references diff --git a/carsus/io/output/photo_ionization.py b/carsus/io/output/photo_ionization.py index f620d4e4c..ba64b2a86 100644 --- a/carsus/io/output/photo_ionization.py +++ b/carsus/io/output/photo_ionization.py @@ -63,8 +63,8 @@ def cross_sections(self): cross_sections["energy"] = u.Quantity(cross_sections["energy"], "Ry").to( "Hz", equivalencies=u.spectral() - ) - cross_sections["sigma"] = u.Quantity(cross_sections["sigma"], "Mbarn").to("cm2") + ).value + cross_sections["sigma"] = u.Quantity(cross_sections["sigma"], "Mbarn").to("cm2").value cross_sections["level_number"] = cross_sections["level_number"].astype("int") cross_sections = cross_sections.rename( columns={"energy": "nu", "sigma": "x_sect"} diff --git a/carsus/io/tests/test_cmfgen.py b/carsus/io/tests/test_cmfgen.py index 35e852e1e..57472f705 100644 --- a/carsus/io/tests/test_cmfgen.py +++ b/carsus/io/tests/test_cmfgen.py @@ -17,7 +17,6 @@ data_dir = os.path.join(os.path.dirname(__file__), "data") -@pytest.mark.with_refdata @pytest.fixture() def si1_reader(): return CMFGENReader.from_config( diff --git a/carsus/io/tests/test_ionization_grammar.py b/carsus/io/tests/test_ionization_grammar.py index 25c00de30..1d47aff99 100644 --- a/carsus/io/tests/test_ionization_grammar.py +++ b/carsus/io/tests/test_ionization_grammar.py @@ -10,7 +10,7 @@ ("3/2", 1.5) ]) def test_j(test_input, exp_j): - tkns = J.parseString(test_input) + tkns = J.parse_string(test_input) assert_almost_equal(tkns[0], exp_j) @@ -20,7 +20,7 @@ def test_j(test_input, exp_j): ("1S", 1, "S") ]) def test_ls_term(test_input, exp_mult, exp_l): - tkns = ls_term.parseString(test_input) + tkns = ls_term.parse_string(test_input) assert tkns["mult"] == exp_mult assert tkns["L"] == exp_l @@ -31,7 +31,7 @@ def test_ls_term(test_input, exp_mult, exp_l): ("(0,2)", 0.0, 2.0) ]) def test_jj_term(test_input, exp_first_j, exp_second_j): - tkns = jj_term.parseString(test_input) + tkns = jj_term.parse_string(test_input) assert_almost_equal(tkns["first_J"], exp_first_j) assert_almost_equal(tkns["second_J"], exp_second_j) @@ -42,11 +42,11 @@ def test_jj_term(test_input, exp_first_j, exp_second_j): ("1S*<4>", 1, "S", 1, 4.0) ]) def test_level_w_ls_term(test_input, exp_mult, exp_l, exp_parity, exp_j): - tkns = level.parseString(test_input) + tkns = level.parse_string(test_input) assert tkns["ls_term"]["mult"] == exp_mult assert tkns["ls_term"]["L"] == exp_l assert tkns["parity"] == exp_parity - assert_almost_equal(tkns["J"], exp_j) # This assertion fails because tkns["J"] is a list and exp_j and integer. e.g. [2] == 2 + assert_almost_equal(tkns["J"][0], exp_j) # This assertion fails because tkns["J"] is a list and exp_j and integer. e.g. [2] == 2 # Same thing on lines 62 and 73. @pytest.mark.parametrize("test_input, exp_first_j, exp_second_j, exp_parity, exp_j",[ @@ -55,11 +55,11 @@ def test_level_w_ls_term(test_input, exp_mult, exp_l, exp_parity, exp_j): ("(1/2, 2)*<2>", 0.5, 2.0, 1, 2.0) ]) def test_level_w_jj_term(test_input, exp_first_j, exp_second_j, exp_parity, exp_j): - tkns = level.parseString(test_input) + tkns = level.parse_string(test_input) assert tkns["jj_term"]["first_J"] == exp_first_j assert tkns["jj_term"]["second_J"] == exp_second_j assert tkns["parity"] == exp_parity - assert_almost_equal(tkns["J"], exp_j) + assert_almost_equal(tkns["J"][0], exp_j) @pytest.mark.parametrize("test_input, exp_parity, exp_j",[ @@ -68,9 +68,9 @@ def test_level_w_jj_term(test_input, exp_first_j, exp_second_j, exp_parity, exp_ ("*<2>", 1, 2.0) ]) def test_level_wo_term(test_input, exp_parity, exp_j): - tkns = level.parseString(test_input) + tkns = level.parse_string(test_input) assert tkns["parity"] == exp_parity - assert_almost_equal(tkns["J"], exp_j) + assert_almost_equal(tkns["J"][0], exp_j) @pytest.mark.parametrize("test_input, exp_parity",[ @@ -78,5 +78,5 @@ def test_level_wo_term(test_input, exp_parity, exp_j): ("*", 1) ]) def test_level_wo_term_and_j(test_input, exp_parity): - tkns = level.parseString(test_input) + tkns = level.parse_string(test_input) assert tkns["parity"] == exp_parity \ No newline at end of file diff --git a/carsus/io/tests/test_nist_weightscomp_grammar.py b/carsus/io/tests/test_nist_weightscomp_grammar.py index bb552a309..e41ff40c3 100644 --- a/carsus/io/tests/test_nist_weightscomp_grammar.py +++ b/carsus/io/tests/test_nist_weightscomp_grammar.py @@ -10,7 +10,7 @@ ("6.0151228874", 6.0151228874) ]) def test_float_(test_input, expected): - tkns = float_.parseString(test_input) + tkns = float_.parse_string(test_input) assert_almost_equal(tkns[0], expected) @@ -19,7 +19,7 @@ def test_float_(test_input, expected): ("18.998403163(6)", [18.998403163, 6e-9]) ]) def test_ufloat(test_input, expected): - tkns = ufloat.parseString(test_input) + tkns = ufloat.parse_string(test_input) assert_almost_equal(tkns.nominal_value, expected[0]) assert_almost_equal(tkns.std_dev, expected[1]) @@ -29,7 +29,7 @@ def test_ufloat(test_input, expected): ("27.02644(20)", [27.02644, 20e-5, False]) ]) def test_ufloat_theor(test_input, expected): - tkns = ufloat_theor.parseString(test_input) + tkns = ufloat_theor.parse_string(test_input) assert_almost_equal(tkns.nominal_value, expected[0]) assert_almost_equal(tkns.std_dev, expected[1]) assert tkns.theoretical == expected[2] @@ -40,7 +40,7 @@ def test_ufloat_theor(test_input, expected): ("g, r", 'g r') ]) def test_notes(test_input, expected): - tkns = notes.parseString(test_input) + tkns = notes.parse_string(test_input) assert tkns[0] == expected @@ -49,7 +49,7 @@ def test_notes(test_input, expected): ("22.98976928(2)", [22.98976928, 2e-8, VAL_SD]) ]) def test_atomic_weight_value_uncertainty(test_input, expected): - tkns = atomic_weight.parseString(test_input) + tkns = atomic_weight.parse_string(test_input) assert_almost_equal(tkns.nominal_value, expected[0]) assert_almost_equal(tkns.std_dev, expected[1]) assert tkns.type == expected[2] @@ -59,7 +59,7 @@ def test_atomic_weight_value_uncertainty(test_input, expected): ("[24.304,24.307]", [[24.304,24.307], INTERVAL]) ]) def test_atomic_weight_interval(test_input, expected): - tkns = atomic_weight.parseString(test_input) + tkns = atomic_weight.parse_string(test_input) assert_allclose([tkns.lwr_bnd, tkns.upr_bnd],expected[0]) assert tkns.type == expected[1] @@ -68,7 +68,7 @@ def test_atomic_weight_interval(test_input, expected): ("[226]", [226, STABLE_MASS_NUM]) ]) def test_atomic_weight_stable_mass_num(test_input, expected): - tkns = atomic_weight.parseString(test_input) + tkns = atomic_weight.parse_string(test_input) assert tkns.stable_mass_number == expected[0] assert tkns.type == expected[1] @@ -78,13 +78,13 @@ def test_atomic_weight_stable_mass_num(test_input, expected): ("0.96941(156)", [0.96941, 156e-5]) ]) def test_isotopic_comp(test_input, expected): - tkns = isotopic_comp.parseString(test_input) + tkns = isotopic_comp.parse_string(test_input) assert_almost_equal(tkns.nominal_value, expected[0]) assert_almost_equal(tkns.std_dev, expected[1]) def test_isotopic_comp_one(): - tkns = isotopic_comp.parseString("1") + tkns = isotopic_comp.parse_string("1") assert tkns.nominal_value == 1 assert tkns.std_dev == '' @@ -94,7 +94,7 @@ def test_isotopic_comp_one(): ("39.963998166(60)", [39.963998166, 60e-9, False]) ]) def test_atomic_mass(test_input, expected): - tkns = atomic_mass.parseString(test_input) + tkns = atomic_mass.parse_string(test_input) assert_almost_equal(tkns.nominal_value, expected[0]) assert_almost_equal(tkns.std_dev, expected[1]) assert tkns.theoretical == expected[2] @@ -105,7 +105,7 @@ def test_atomic_mass(test_input, expected): ("Uuo", "Uuo") ]) def test_symbol(test_input, expected): - tkns = symbol.parseString(test_input) + tkns = symbol.parse_string(test_input) assert tkns[0] == expected @@ -115,7 +115,7 @@ def test_symbol(test_input, expected): ("Notes", COLUMN_NAMES_MAPPING["Notes"]) ]) def test_column_name(test_input, expected): - tkns = column_name.parseString(test_input) + tkns = column_name.parse_string(test_input) assert tkns[0] == expected @@ -178,7 +178,7 @@ def test_column_name(test_input, expected): AW_TYPE_COL: STABLE_MASS_NUM, AW_STABLE_MASS_NUM_COL: 222}) ]) def test_isotope(test_input, expected): - tkns = isotope.parseString(test_input) + tkns = isotope.parse_string(test_input) tkns_dict = to_flat_dict(tkns) for key, item in tkns_dict.items(): if isinstance(item, float): diff --git a/carsus/io/tests/test_util.py b/carsus/io/tests/test_util.py index 4290f4913..af3da2349 100644 --- a/carsus/io/tests/test_util.py +++ b/carsus/io/tests/test_util.py @@ -11,7 +11,7 @@ {'atomic_weight_nominal_value':'6.8083492038', 'atomic_weight_std_dev':'23'}) ]) def test_to_flat_dict(test_input, expected, entry): - tkns = entry.parseString(test_input) + tkns = entry.parse_string(test_input) tkns_dict = to_flat_dict(tkns) assert tkns_dict == expected diff --git a/carsus/io/zeta.py b/carsus/io/zeta.py index 95c20989a..e4330a1cd 100644 --- a/carsus/io/zeta.py +++ b/carsus/io/zeta.py @@ -35,7 +35,7 @@ def _prepare_data(self): usecols=range(1, 23), names=names, comment="#", - delim_whitespace=True) + sep=r"\s+") self.base = ( pd.DataFrame(zeta_df).set_index( @@ -43,4 +43,4 @@ def _prepare_data(self): ) columns = [float(c) for c in self.base.columns] - self.base.columns = pd.Float64Index(columns, name="temp") + self.base.columns = pd.Index(columns, name="temp", dtype=np.float64) diff --git a/carsus/util/hash.py b/carsus/util/hash.py index cc7815471..89e61e941 100644 --- a/carsus/util/hash.py +++ b/carsus/util/hash.py @@ -1,24 +1,19 @@ -import pyarrow as pa import hashlib +import pickle def serialize_pandas_object(pd_object): - """Serialize Pandas objects with PyArrow. + """Serialize Pandas objects with Pickle. Parameters ---------- pd_object : pandas.Series or pandas.DataFrame - Pandas object to be serialized with PyArrow. + Pandas object to be serialized with Pickle. Returns ------- - pyarrow.lib.SerializedPyObject - PyArrow serialized Python object. + Pickle serialized Python object. """ - - context = pa.default_serialization_context() - serialized_pd_object = context.serialize(pd_object) - - return serialized_pd_object + return pickle.dumps(pd_object) def hash_pandas_object(pd_object, algorithm="md5"): @@ -49,6 +44,4 @@ def hash_pandas_object(pd_object, algorithm="md5"): else: raise ValueError('algorithm not supported') - buffer = serialize_pandas_object(pd_object).to_buffer() - - return hash_func(buffer).hexdigest() \ No newline at end of file + return hash_func(serialize_pandas_object(pd_object)).hexdigest() \ No newline at end of file diff --git a/carsus/util/helpers.py b/carsus/util/helpers.py index 11dc2779c..d684ae117 100644 --- a/carsus/util/helpers.py +++ b/carsus/util/helpers.py @@ -11,8 +11,8 @@ def get_data_path(fname): os.path.dirname(carsus.__file__), 'data', fname ) -ATOMIC_SYMBOLS_DATA = np.recfromtxt(get_data_path('basic_atomic_data.csv'), skip_header=1, - delimiter=',', usecols=(0, 1), names=['atomic_number', 'symbol'], encoding='utf-8') +ATOMIC_SYMBOLS_DATA = np.genfromtxt(get_data_path('basic_atomic_data.csv'), skip_header=1, + delimiter=',', usecols=(0, 1), names=['atomic_number', 'symbol'], encoding='utf-8', dtype=None) SYMBOL2ATOMIC_NUMBER = OrderedDict(zip(ATOMIC_SYMBOLS_DATA['symbol'], ATOMIC_SYMBOLS_DATA['atomic_number'])) diff --git a/carsus/util/selected.py b/carsus/util/selected.py index 7ce36c797..b1c713943 100644 --- a/carsus/util/selected.py +++ b/carsus/util/selected.py @@ -106,7 +106,7 @@ def parse_selected_atoms(atoms): [1, 3, 4, 5, 6, 7, 14, 16] """ - return selected_atoms.parseString(atoms).asList() + return selected_atoms.parse_string(atoms).asList() def parse_selected_species(species): @@ -147,4 +147,4 @@ def parse_selected_species(species): [(5, 4), (6, 4), (6, 5), (7, 4), (7, 5), (8, 4), (8, 5)] """ - return selected_species.parseString(species).asList() + return selected_species.parse_string(species).asList() diff --git a/carsus/util/tests/test_hash.py b/carsus/util/tests/test_hash.py index 9612d15bf..bad27ba42 100644 --- a/carsus/util/tests/test_hash.py +++ b/carsus/util/tests/test_hash.py @@ -1,14 +1,13 @@ import pytest -import hashlib import pandas as pd -from carsus.util import serialize_pandas_object, hash_pandas_object +from carsus.util import hash_pandas_object @pytest.mark.parametrize( "values, md5", [ - ([(0, 1), (1, 2), (2, 3), (3, 4)], "a703629383"), - (["apple", "banana", "orange"], "24e45baf79"), + ([(0, 1), (1, 2), (2, 3), (3, 4)], "12b31eadd7"), + (["apple", "banana", "orange"], "89b33d7168"), ], ) def test_hash_pd(values, md5): diff --git a/carsus/util/tests/test_selected.py b/carsus/util/tests/test_selected.py index d5faba50b..140d18535 100644 --- a/carsus/util/tests/test_selected.py +++ b/carsus/util/tests/test_selected.py @@ -12,7 +12,7 @@ ("h", 1) ]) def test_element(test_input, exp_atomic_number): - tokens = element.parseString(test_input) + tokens = element.parse_string(test_input) assert tokens[0] == exp_atomic_number @@ -22,7 +22,7 @@ def test_element(test_input, exp_atomic_number): ("si-s", [14, 15, 16]) ]) def test_element_range(test_input, exp_atomic_numbers): - tokens = element_range.parseString(test_input) + tokens = element_range.parse_string(test_input) assert tokens.asList() == exp_atomic_numbers @@ -33,7 +33,7 @@ def test_element_range(test_input, exp_atomic_numbers): ('he, h-li', [1, 2, 3]) ]) def test_selected_atoms(test_input, exp_atomic_numbers): - tokens = selected_atoms.parseString(test_input) + tokens = selected_atoms.parse_string(test_input) assert tokens.asList() == exp_atomic_numbers @@ -65,7 +65,7 @@ def test_parse_selected_atoms_raises_invalid(invalid_selected_atoms): ('H-Li', [(1, 0), (2, 0), (2, 1), (3, 0), (3, 1), (3, 2)]) ]) def test_parse_species_entry(test_input, expected_list): - tokens = species_entry.parseString(test_input) + tokens = species_entry.parse_string(test_input) assert tokens.asList() == expected_list diff --git a/carsus_env3.yml b/carsus_env3.yml index 9c59f5148..4bb8c08e1 100644 --- a/carsus_env3.yml +++ b/carsus_env3.yml @@ -4,26 +4,23 @@ channels: - conda-forge dependencies: - - python =3.7 + - python - setuptools - setuptools_scm - pip - - numpy =1.15 - - pandas =1.0 - - astropy =3 - - chiantipy =0.8.4 + - numpy + - pandas + - astropy + - chiantipy # I/O - pyyaml - uncertainties - - pyparsing =2.2 - - sqlalchemy =1.2 + - pyparsing - beautifulsoup4 - html5lib - h5py - pytables - - pyarrow =0.14.1 - - glog =0.5 # https://github.com/google/glog/issues/814 - requests - roman @@ -51,8 +48,13 @@ dependencies: # Test/Coverage - pytest - pytest-cov + - pytest-html - pytest-astropy - - epassaro::pytest-arraydiff + - coverage + + # Code quality + - black =22.3 + - ruff # Other - git-lfs diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 8b1751d81..762f8387f 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,270 +1,362 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 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--arraydiff-reference-path=carsus-refdata/arraydiff` - Run tests marked with ``@pytest.mark.array_compare`` decorator. - The tests would look for reference files in the refdata folder which can be generated using the above option. - diff --git a/pytest.ini b/pytest.ini index 6d7806016..aeba9a6d1 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,4 +1,3 @@ [pytest] markers = with_refdata: mark tests as needing refdata path to run - with_test_db: mark tests as needing test_db path to run