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rename gmapi to gmapy
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gschnabel committed Oct 24, 2022
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2 changes: 1 addition & 1 deletion examples/example-001-run-gmap.py
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Expand Up @@ -20,7 +20,7 @@
############################################################

import argparse
from gmapi.legacy.legacy_gmap import run_gmap
from gmapy.legacy.legacy_gmap import run_gmap


if __name__ == '__main__':
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4 changes: 2 additions & 2 deletions examples/example-002-chisquare-calc.ipynb
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Expand Up @@ -22,8 +22,8 @@
"source": [
"import numpy as np\n",
"from scipy.sparse.linalg import spsolve\n",
"from gmapi.legacy.legacy_gmap import run_gmap\n",
"from gmapi.mappings.compound_map import CompoundMap\n",
from gmapy.legacy.legacy_gmap import run_gmap\n",
from gmapy.mappings.compound_map import CompoundMap\n",
"dbfile = '../tests/testdata/data-2017-07-26.gma'"
]
},
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4 changes: 2 additions & 2 deletions examples/example-003-plot-evaluation-results.ipynb
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Expand Up @@ -24,8 +24,8 @@
"import pandas as pd\n",
"from numpy.random import default_rng\n",
"import matplotlib.pyplot as plt\n",
"from gmapi.legacy.legacy_gmap import run_gmap\n",
"from gmapi.mappings.compound_map import CompoundMap\n",
from gmapy.legacy.legacy_gmap import run_gmap\n",
from gmapy.mappings.compound_map import CompoundMap\n",
"dbfile = '../tests/testdata/data-2017-07-26.gma'"
]
},
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2 changes: 1 addition & 1 deletion examples/example-004-python-versus-fortran-gmap.ipynb
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Expand Up @@ -21,7 +21,7 @@
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"from gmapi.legacy.legacy_gmap import run_gmap"
from gmapy.legacy.legacy_gmap import run_gmap"
]
},
{
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4 changes: 2 additions & 2 deletions examples/example-005-compute-sacs-results.ipynb
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Expand Up @@ -21,7 +21,7 @@
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"from gmapi.legacy.legacy_gmap import run_gmap"
from gmapy.legacy.legacy_gmap import run_gmap"
]
},
{
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}
],
"source": [
"from gmapi.mappings.compound_map import CompoundMap\n",
from gmapy.mappings.compound_map import CompoundMap\n",
"compmap = CompoundMap(fix_sacs_jacobian=True)\n",
"predvals1 = compmap.propagate(syntable1, syntable1.POST.to_numpy())\n",
"predvals2 = compmap.propagate(syntable2, syntable2.POST.to_numpy())\n",
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10 changes: 5 additions & 5 deletions examples/example-006-gmap-with-ratio-of-sacs.py
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@@ -1,11 +1,11 @@
import sys
sys.path.append('..')
from gmapi.data_management.dataset import Dataset
from gmapi.data_management.datablock import Datablock
from gmapi.data_management.datablock_list import DatablockList
from gmapy.data_management.dataset import Dataset
from gmapy.data_management.datablock import Datablock
from gmapy.data_management.datablock_list import DatablockList
import numpy as np
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

# read the database of standards 2017 and perform the gls fitting
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6 changes: 3 additions & 3 deletions examples/standard_studies/analysis_001/analysis_after_2017.py
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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6 changes: 3 additions & 3 deletions examples/standard_studies/analysis_002/gmap_fit_2017.py
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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6 changes: 3 additions & 3 deletions examples/standard_studies/analysis_002/gmap_fit_latest.py
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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6 changes: 3 additions & 3 deletions examples/standard_studies/analysis_002/gmap_fit_modified.py
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Expand Up @@ -3,9 +3,9 @@
sys.path.append('../..')
sys.path.append('../../..')
from copy import deepcopy
from gmapi.data_management.datablock_list import DatablockList
from gmapi.gmap import run_gmap_simplified
from gmapi.data_management.database_IO import (read_json_gma_database,
from gmapy.data_management.datablock_list import DatablockList
from gmapy.gmap import run_gmap_simplified
from gmapy.data_management.database_IO import (read_json_gma_database,
read_legacy_gma_database)

from utils.convenience_funs import (get_sacs_predictions,
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8 changes: 4 additions & 4 deletions examples/standard_studies/utils/convenience_funs.py
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Expand Up @@ -4,10 +4,10 @@
from copy import deepcopy
import pandas as pd
import numpy as np
from gmapi.data_management.dataset import Dataset
from gmapi.data_management.datablock import Datablock
from gmapi.data_management.datablock_list import DatablockList
from gmapi.mappings.compound_map import CompoundMap
from gmapy.data_management.dataset import Dataset
from gmapy.data_management.datablock import Datablock
from gmapy.data_management.datablock_list import DatablockList
from gmapy.mappings.compound_map import CompoundMap
import json


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2 changes: 1 addition & 1 deletion examples/standard_studies/utils/r_adapter.py
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Expand Up @@ -2,7 +2,7 @@
sys.path.append('..')
sys.path.append('../..')
sys.path.append('../../..')
from gmapi.mappings.compound_map import CompoundMap
from gmapy.mappings.compound_map import CompoundMap
import numpy as np
import pandas as pd

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2 changes: 1 addition & 1 deletion legacy-tests/test_001/run_test.sh
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Expand Up @@ -67,7 +67,7 @@ cd result/python/
PYTHONPATH="$GMAP_python_dir"
python -c '
import pandas as pd
from gmapi.legacy.legacy_gmap import run_gmap;
from gmapy.legacy.legacy_gmap import run_gmap;
res = run_gmap(dbfile="data.gma", dbtype="legacy",
fix_ppp_bug=False, fix_sacs_jacobian=False,
legacy_output=True)
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2 changes: 1 addition & 1 deletion legacy-tests/test_002/run_test.sh
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Expand Up @@ -67,7 +67,7 @@ cd result/python/
PYTHONPATH="$GMAP_python_dir"
python -c '
import pandas as pd
from gmapi.legacy.legacy_gmap import run_gmap;
from gmapy.legacy.legacy_gmap import run_gmap;
res = run_gmap(dbfile="gmadata.json", dbtype="json",
fix_ppp_bug=False, fix_sacs_jacobian=False,
legacy_output=True)
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2 changes: 1 addition & 1 deletion legacy-tests/test_003/run_test.sh
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Expand Up @@ -67,7 +67,7 @@ cd result/python/
PYTHONPATH="$GMAP_python_dir"
python -c '
import pandas as pd
from gmapi.legacy.legacy_gmap import run_gmap;
from gmapy.legacy.legacy_gmap import run_gmap;
res = run_gmap(dbfile="gmadata.json", dbtype="json",
fix_ppp_bug=False, fix_sacs_jacobian=False,
legacy_output=True)
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2 changes: 1 addition & 1 deletion legacy-tests/test_004/run_test.sh
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Expand Up @@ -67,7 +67,7 @@ cd result/python/
PYTHONPATH="$GMAP_python_dir"
python -c '
import pandas as pd
from gmapi.legacy.legacy_gmap import run_gmap;
from gmapy.legacy.legacy_gmap import run_gmap;
res = run_gmap(dbfile="data.gma", dbtype="legacy",
fix_ppp_bug=False, fix_sacs_jacobian=False,
legacy_output=True)
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2 changes: 1 addition & 1 deletion legacy-tests/test_005/run_test.sh
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Expand Up @@ -67,7 +67,7 @@ cd result/python/
PYTHONPATH="$GMAP_python_dir"
python -c '
import pandas as pd
from gmapi.legacy.legacy_gmap import run_gmap;
from gmapy.legacy.legacy_gmap import run_gmap;
res = run_gmap(dbfile="gmadata.json", dbtype="json", correct_ppp=False,
fix_sacs_jacobian=False, legacy_output=True)
res["table"].to_csv("restable.csv", sep=";")
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3 changes: 1 addition & 2 deletions pyproject.toml
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@@ -1,5 +1,5 @@
[tool.poetry]
name = "gmapi"
name = "gmapy"
version = "0.13"
description = "package to evaluate cross sections"
authors = ["Georg Schnabel"]
Expand All @@ -14,7 +14,6 @@ scipy = "^1.9.1"
fortranformat = "^1.2.2"
scikit-sparse = "^0.4.6"


[tool.poetry.group.dev.dependencies]
pytest = "^7.1.3"
openpyxl = "^3.0.10"
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4 changes: 2 additions & 2 deletions tests/test_basic_integral_mappings.py
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@@ -1,8 +1,8 @@
import unittest
import numpy as np
from gmapi.mappings.basic_integral_maps import (basic_integral_propagate,
from gmapy.mappings.basic_integral_maps import (basic_integral_propagate,
get_basic_integral_sensmat)
from gmapi.mappings.helperfuns import numeric_jacobian
from gmapy.mappings.helperfuns import numeric_jacobian


class TestBasicIntegralMapping(unittest.TestCase):
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6 changes: 3 additions & 3 deletions tests/test_basic_integral_of_product_mappings.py
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@@ -1,10 +1,10 @@
import unittest
import numpy as np
from gmapi.mappings.basic_maps import basic_propagate
from gmapi.mappings.basic_integral_maps import (
from gmapy.mappings.basic_maps import basic_propagate
from gmapy.mappings.basic_integral_maps import (
basic_integral_of_product_propagate,
get_basic_integral_of_product_sensmats)
from gmapi.mappings.helperfuns import numeric_jacobian, compute_romberg_integral
from gmapy.mappings.helperfuns import numeric_jacobian, compute_romberg_integral


class TestBasicIntegralOfProductMapping(unittest.TestCase):
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4 changes: 2 additions & 2 deletions tests/test_basic_mappings.py
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@@ -1,9 +1,9 @@
import unittest
import numpy as np
from scipy.sparse import csr_matrix
from gmapi.mappings.basic_maps import (basic_propagate, get_basic_sensmat,
from gmapy.mappings.basic_maps import (basic_propagate, get_basic_sensmat,
basic_multiply_Sdic_rows, basic_extract_Sdic_coeffs)
from gmapi.mappings.helperfuns import numeric_jacobian, return_matrix
from gmapy.mappings.helperfuns import numeric_jacobian, return_matrix


class TestBasicMappingsPropagation(unittest.TestCase):
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4 changes: 2 additions & 2 deletions tests/test_basic_product_mapping.py
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@@ -1,8 +1,8 @@
import unittest
import numpy as np
from gmapi.mappings.basic_maps import (basic_propagate, basic_product_propagate,
from gmapy.mappings.basic_maps import (basic_propagate, basic_product_propagate,
get_basic_product_sensmats)
from gmapi.mappings.helperfuns import numeric_jacobian
from gmapy.mappings.helperfuns import numeric_jacobian


class TestBasicProductPropagate(unittest.TestCase):
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6 changes: 3 additions & 3 deletions tests/test_conversions.py
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Expand Up @@ -3,9 +3,9 @@
from tempfile import TemporaryDirectory
import numpy as np

from gmapi.legacy.legacy_gmap import run_gmap
from gmapi.legacy.database_reading import read_gma_database
from gmapi.legacy.conversion_utils import (sanitize_datablock,
from gmapy.legacy.legacy_gmap import run_gmap
from gmapy.legacy.database_reading import read_gma_database
from gmapy.legacy.conversion_utils import (sanitize_datablock,
desanitize_datablock, compare_legacy_datablock_lists,
augment_datablocks_with_NTOT, sanitize_prior,
desanitize_prior, convert_GMA_database_to_JSON)
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2 changes: 1 addition & 1 deletion tests/test_gma_database_class.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import unittest
import pathlib
import pandas as pd
from gmapi.gma_database_class import GMADatabase
from gmapy.gma_database_class import GMADatabase
import numpy as np
from copy import deepcopy
from scipy.sparse import csr_matrix
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6 changes: 3 additions & 3 deletions tests/test_gma_database_usu_class.py
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@@ -1,14 +1,14 @@
import unittest
import pathlib
import pandas as pd
from gmapi.gma_database_usu_class import GMADatabaseUSU
from gmapy.gma_database_usu_class import GMADatabaseUSU
import numpy as np
from copy import deepcopy
from scipy.sparse import csr_matrix
from sksparse.cholmod import cholesky
from gmapi.mappings.helperfuns import numeric_jacobian
from gmapy.mappings.helperfuns import numeric_jacobian

from gmapi.optimization_auxfuns import create_posterior_funs
from gmapy.optimization_auxfuns import create_posterior_funs


# NOTE: This test case tests at present tests mostly the functionality
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4 changes: 2 additions & 2 deletions tests/test_gmap_simplified.py
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Expand Up @@ -2,8 +2,8 @@
import pathlib
import numpy as np
from pandas.testing import assert_frame_equal
from gmapi.gmap import run_gmap_simplified
from gmapi.legacy.legacy_gmap import run_gmap
from gmapy.gmap import run_gmap_simplified
from gmapy.legacy.legacy_gmap import run_gmap


class TestGmapSimplified(unittest.TestCase):
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14 changes: 7 additions & 7 deletions tests/test_inference.py
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Expand Up @@ -4,15 +4,15 @@
import pandas as pd
from scipy.sparse import coo_matrix, csr_matrix

from gmapi.legacy.database_reading import read_gma_database
from gmapi.legacy.conversion_utils import (sanitize_datablock, sanitize_prior)
from gmapi.data_management.uncfuns import (create_relunc_vector,
from gmapy.legacy.database_reading import read_gma_database
from gmapy.legacy.conversion_utils import (sanitize_datablock, sanitize_prior)
from gmapy.data_management.uncfuns import (create_relunc_vector,
create_experimental_covmat)
from gmapi.data_management.tablefuns import (create_prior_table,
from gmapy.data_management.tablefuns import (create_prior_table,
create_experiment_table)
from gmapi.mappings.priortools import attach_shape_prior
from gmapi.inference import gls_update
from gmapi.mappings.compound_map import CompoundMap
from gmapy.mappings.priortools import attach_shape_prior
from gmapy.inference import gls_update
from gmapy.mappings.compound_map import CompoundMap


class TestInference(unittest.TestCase):
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