From e7eb67957282d47ecf037a6391e006e2369c6620 Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Wed, 13 Nov 2024 12:30:06 -0500 Subject: [PATCH 1/5] fix missing C2 --- carsus/io/vald/vald.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/carsus/io/vald/vald.py b/carsus/io/vald/vald.py index 4e2970585..89adba6cf 100644 --- a/carsus/io/vald/vald.py +++ b/carsus/io/vald/vald.py @@ -166,7 +166,7 @@ def read_vald_raw(self, fname=None): # Elm Ion WL_air(A) log gf* E_low(eV) J lo E_up(eV) J up lower upper mean Rad. Stark Waals # 'TiO 1', 4100.00020, -11.472, 0.2011, 31.0, 3.2242, 32.0, 99.000, 99.000, 99.000, 6.962, 0.000, 0.000, - DATA_RE_PATTERN = re.compile("'[a-zA-Z]+ \d+',[\s*-?\d+[\.\d+]+,]*") + DATA_RE_PATTERN = re.compile("'[a-zA-Z]+\d* \d+',[\s*-?\d+[\.\d+]+,]*") buffer, checksum = read_from_buffer(self.fname) content = buffer.read().decode() From 6cc0707b7250b448b64b546d0e23fddc2690572a Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Wed, 13 Nov 2024 12:36:33 -0500 Subject: [PATCH 2/5] fix test --- carsus/io/tests/test_vald.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/carsus/io/tests/test_vald.py b/carsus/io/tests/test_vald.py index fa51da465..9c1fba233 100644 --- a/carsus/io/tests/test_vald.py +++ b/carsus/io/tests/test_vald.py @@ -65,7 +65,9 @@ def test_vald_reader_vald_raw(vald_raw, index, wl_air, log_gf, e_low, e_up): ], ) def test_vald_reader_vald(vald, index, wl_air, log_gf, e_low, e_up, ion_charge): - row = vald[1].loc[ + row = vald[ + 1 + ].loc[ index ] # vald is a length two array. The first element is the atoms and the second is the molecules assert_almost_equal(row["WL_air(A)"], wl_air) @@ -133,7 +135,7 @@ def test_vald_short_stellar_linelist_molecules( v_mic, ion_charge, ): - assert len(vald_linelist_molecules_short_form_stellar) == 94 + assert len(vald_linelist_molecules_short_form_stellar) == 95 row = vald_linelist_molecules_short_form_stellar.iloc[index] assert_almost_equal(row["wavelength"], wavelength) assert_allclose( From 1e99b0f67bc6798be0c2f04adc6eed9d50497bac Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Wed, 13 Nov 2024 12:41:07 -0500 Subject: [PATCH 3/5] apply formatting --- carsus/io/tests/test_vald.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/carsus/io/tests/test_vald.py b/carsus/io/tests/test_vald.py index 9c1fba233..dbafde8e0 100644 --- a/carsus/io/tests/test_vald.py +++ b/carsus/io/tests/test_vald.py @@ -65,9 +65,7 @@ def test_vald_reader_vald_raw(vald_raw, index, wl_air, log_gf, e_low, e_up): ], ) def test_vald_reader_vald(vald, index, wl_air, log_gf, e_low, e_up, ion_charge): - row = vald[ - 1 - ].loc[ + row = vald[1].loc[ index ] # vald is a length two array. The first element is the atoms and the second is the molecules assert_almost_equal(row["WL_air(A)"], wl_air) From 1a2cfe49f4c278c0c55b9ed66907e178348b6d71 Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Wed, 13 Nov 2024 14:39:36 -0500 Subject: [PATCH 4/5] raw string regex --- carsus/io/vald/vald.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/carsus/io/vald/vald.py b/carsus/io/vald/vald.py index 89adba6cf..bceb092b0 100644 --- a/carsus/io/vald/vald.py +++ b/carsus/io/vald/vald.py @@ -166,7 +166,7 @@ def read_vald_raw(self, fname=None): # Elm Ion WL_air(A) log gf* E_low(eV) J lo E_up(eV) J up lower upper mean Rad. Stark Waals # 'TiO 1', 4100.00020, -11.472, 0.2011, 31.0, 3.2242, 32.0, 99.000, 99.000, 99.000, 6.962, 0.000, 0.000, - DATA_RE_PATTERN = re.compile("'[a-zA-Z]+\d* \d+',[\s*-?\d+[\.\d+]+,]*") + DATA_RE_PATTERN = re.compile(r"'[a-zA-Z]+\d* \d+',[\s*-?\d+[\.\d+]+,]*") buffer, checksum = read_from_buffer(self.fname) content = buffer.read().decode() From c39c8b45537f2c709f5bb07e69154a939e3d39c7 Mon Sep 17 00:00:00 2001 From: Josh Shields Date: Wed, 13 Nov 2024 15:01:55 -0500 Subject: [PATCH 5/5] add comment for pattern --- carsus/io/vald/vald.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/carsus/io/vald/vald.py b/carsus/io/vald/vald.py index bceb092b0..47b1ac392 100644 --- a/carsus/io/vald/vald.py +++ b/carsus/io/vald/vald.py @@ -166,7 +166,9 @@ def read_vald_raw(self, fname=None): # Elm Ion WL_air(A) log gf* E_low(eV) J lo E_up(eV) J up lower upper mean Rad. Stark Waals # 'TiO 1', 4100.00020, -11.472, 0.2011, 31.0, 3.2242, 32.0, 99.000, 99.000, 99.000, 6.962, 0.000, 0.000, - DATA_RE_PATTERN = re.compile(r"'[a-zA-Z]+\d* \d+',[\s*-?\d+[\.\d+]+,]*") + DATA_RE_PATTERN = re.compile( + r"'[a-zA-Z]+\d* \d+',[\s*-?\d+[\.\d+]+,]*" + ) # This matches to the Elm Ion field of the format above (e.g., TiO 1 or C 2) buffer, checksum = read_from_buffer(self.fname) content = buffer.read().decode()