psdi-data-conversion 0.2.1__py3-none-any.whl → 0.2.2__py3-none-any.whl

psdi_data_conversion/converters/base.py

@@ -20,6 +20,7 @@ from typing import Any
 from psdi_data_conversion import constants as const
 from psdi_data_conversion import log_utility
 from psdi_data_conversion.dist import bin_exists, get_bin_path, get_dist
+from psdi_data_conversion.file_io import get_package_path
 from psdi_data_conversion.security import SAFE_STRING_RE, string_is_safe
 
 try:
@@ -744,7 +745,9 @@ class ScriptFileConverter(FileConverter):
         if self.required_bin is not None:
             env["BIN_PATH"] = get_bin_path(self.required_bin)
 
-        process = subprocess.run(['sh', f'psdi_data_conversion/scripts/{self.script}', *self._get_script_args()],
+        script_abs_path = os.path.join(get_package_path(), "scripts", self.script)
+
+        process = subprocess.run(['sh', script_abs_path, *self._get_script_args()],
                                  env=env, capture_output=True, text=True)
 
         self.out = process.stdout

psdi_data_conversion/database.py

@@ -24,6 +24,7 @@ from psdi_data_conversion import constants as const
 from psdi_data_conversion.converter import (L_REGISTERED_CONVERTERS, L_SUPPORTED_CONVERTERS,
                                             get_registered_converter_class)
 from psdi_data_conversion.converters.base import FileConverter, FileConverterException
+from psdi_data_conversion.file_io import get_package_path
 from psdi_data_conversion.utils import regularize_name
 
 # Keys for top-level and general items in the database
@@ -1206,10 +1207,7 @@ def get_database_path() -> str:
     str
     """
 
-    # For an interactive shell, __file__ won't be defined for this module, so use the constants module instead
-    reference_file = os.path.realpath(const.__file__)
-
-    qualified_database_filename = os.path.join(os.path.dirname(reference_file), const.DATABASE_FILENAME)
+    qualified_database_filename = os.path.join(get_package_path(), const.DATABASE_FILENAME)
 
     return qualified_database_filename
 

psdi_data_conversion/dist.py

@@ -9,7 +9,7 @@ import os
 import shutil
 import sys
 
-import psdi_data_conversion
+from psdi_data_conversion.file_io import get_package_path
 
 # Labels for each platform (which we use for the folder in this project), and the head of the name each platform will
 # have in `sys.platform`
@@ -29,7 +29,7 @@ D_DIST_NAME_HEADS = {LINUX_LABEL: LINUX_NAME_HEAD,
 
 
 # Determine the fully-qualified binary directory when this module is first imported
-BIN_DIR: str = os.path.join(psdi_data_conversion.__path__[0], "bin")
+BIN_DIR: str = os.path.join(get_package_path(), "bin")
 
 
 def get_dist():

psdi_data_conversion/file_io.py

@@ -7,12 +7,30 @@ Functions and classes related to general filesystem input/output
 
 import glob
 import os
+from functools import lru_cache
 from shutil import copyfile, make_archive, unpack_archive
 from tempfile import TemporaryDirectory
 
 from psdi_data_conversion import constants as const
 
 
+@lru_cache(maxsize=1)
+def get_package_path() -> str:
+    """Gets the absolute path to where the `psdi_data_conversion` package is on disk
+
+    Returns
+    -------
+    str
+    """
+
+    # For an interactive shell, __file__ won't be defined for this module, so use the constants module instead
+    reference_file = os.path.realpath(const.__file__)
+
+    package_path = os.path.dirname(reference_file)
+
+    return package_path
+
+
 def is_archive(filename: str) -> bool:
     """Uses a file's extension to check if it's an archive or not
     """

psdi_data_conversion/testing/constants.py

@@ -9,7 +9,7 @@ import os
 # Locations relative to the root directory of the project - to ensure the files are found, tests should chdir to this
 # directory before searching for files
 
-TEST_DATA_LOC_IN_PROJECT = "./test_data"
+TEST_DATA_LOC_IN_PROJECT = "test_data"
 
 INPUT_TEST_DATA_LOC_IN_PROJECT = TEST_DATA_LOC_IN_PROJECT
 OUTPUT_TEST_DATA_LOC_IN_PROJECT = os.path.join(TEST_DATA_LOC_IN_PROJECT, "output")

psdi_data_conversion/testing/utils.py

@@ -11,6 +11,7 @@ import shlex
 import sys
 from collections.abc import Callable, Iterable
 from dataclasses import dataclass, field
+from functools import lru_cache
 from math import isclose
 from tempfile import TemporaryDirectory
 from typing import Any
@@ -19,32 +20,43 @@ from unittest.mock import patch
 import py
 import pytest
 
-import psdi_data_conversion
 from psdi_data_conversion.constants import CONVERTER_DEFAULT, GLOBAL_LOG_FILENAME, LOG_NONE, OUTPUT_LOG_EXT
 from psdi_data_conversion.converter import run_converter
 from psdi_data_conversion.converters.openbabel import COORD_GEN_KEY, COORD_GEN_QUAL_KEY
 from psdi_data_conversion.database import get_format_info
 from psdi_data_conversion.dist import LINUX_LABEL, get_dist
-from psdi_data_conversion.file_io import is_archive, split_archive_ext
+from psdi_data_conversion.file_io import get_package_path, is_archive, split_archive_ext
 from psdi_data_conversion.main import main as data_convert_main
 from psdi_data_conversion.testing.constants import (INPUT_TEST_DATA_LOC_IN_PROJECT, OUTPUT_TEST_DATA_LOC_IN_PROJECT,
                                                     TEST_DATA_LOC_IN_PROJECT)
 
 
-def get_path_in_project(filename):
-    """Get the realpath to a file contained within the project, given its project-relative path"""
+@lru_cache(maxsize=1)
+def get_project_path() -> str:
+    """Gets the absolute path to where the project is on disk, using the package path to find it and checking that it
+    contains the expected files
+
+    Returns
+    -------
+    str
+    """
 
-    old_cwd = os.getcwd()
+    project_path = os.path.abspath(os.path.join(get_package_path(), ".."))
 
-    try:
-        os.chdir(os.path.join(psdi_data_conversion.__path__[0], ".."))
-        realpath = os.path.realpath(filename)
+    # Check that the project path contains the expected test_data folder
+    if not os.path.isdir(os.path.join(project_path, TEST_DATA_LOC_IN_PROJECT)):
+        raise FileNotFoundError(f"Project path was expected to be '{project_path}', but this does not contain the "
+                                f"expected directory '{TEST_DATA_LOC_IN_PROJECT}'")
 
-    finally:
-        # Change back to the previous directory
-        os.chdir(old_cwd)
+    return project_path
+
+
+def get_path_in_project(filename):
+    """Get the realpath to a file contained within the project, given its project-relative path"""
+
+    abs_path = os.path.abspath(os.path.join(get_project_path(), filename))
 
-    return realpath
+    return abs_path
 
 
 def get_test_data_loc():
@@ -567,7 +579,7 @@ def check_file_match(filename: str, ex_filename: str) -> str:
 
     # Read in both files
     text = open(filename, "r").read()
-    ex_text = open(ex_filename, "r").read()
+    ex_text = open(get_path_in_project(ex_filename), "r").read()
 
     # We want to check they're the same without worrying about whitespace (which doesn't matter for this format),
     # so we accomplish this by using the string's `split` method, which splits on whitespace by default

{psdi_data_conversion-0.2.1.dist-info → psdi_data_conversion-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: psdi_data_conversion
-Version: 0.2.1
+Version: 0.2.2
 Summary: Chemistry file format conversion service, provided by PSDI
 Project-URL: Homepage, https://data-conversion.psdi.ac.uk/
 Project-URL: Documentation, https://psdi-uk.github.io/psdi-data-conversion/

{psdi_data_conversion-0.2.1.dist-info → psdi_data_conversion-0.2.2.dist-info}/RECORD

@@ -2,9 +2,9 @@ psdi_data_conversion/__init__.py,sha256=urMsTqsTHTch1q4rMT9dgGnrvdPFMP9B8r-6Kr8H
 psdi_data_conversion/app.py,sha256=VmZlIAZ_J9W6p_WUcTA_2UNmZxssmq1aT72I2d1ObDc,3606
 psdi_data_conversion/constants.py,sha256=eXE43_9YFahoehiUV7FtqN9MKb-UpSfY2win9ic9W8I,7348
 psdi_data_conversion/converter.py,sha256=OlwGKxI8nj76wrlVzP5S7fpXb6L-Ql8-mYLYGhW81Fk,27816
-psdi_data_conversion/database.py,sha256=7Xm5e8Wi3b2wGUh2soBZ4DdJ0PhVSXAvv1dVCXDhNQg,65685
-psdi_data_conversion/dist.py,sha256=LOcKEP7H7JA9teX1m-5awuBi69gmdhtUit7yxtCTOZ8,2293
-psdi_data_conversion/file_io.py,sha256=LvdPmnYL_7Xlcr-7LJjUbbky4gKiqTTvPRzdbtvQaJo,8794
+psdi_data_conversion/database.py,sha256=0hSuvjpgj6OApNXhEPTzD4VAS8UY00RdtpFkaFsVXho,65564
+psdi_data_conversion/dist.py,sha256=Db7mbLLANfugaptrcWCoVddwHT2rdP4X4HuP6uxr9AI,2309
+psdi_data_conversion/file_io.py,sha256=SE7cXVedm5ZLdxDQ7W7L2R9LXTqJz2Tak9-YTvc7_js,9250
 psdi_data_conversion/log_utility.py,sha256=CHAq-JvBnTKaE0SHK5hM5j2dTbfSli4iUc3hsf6dBhc,8789
 psdi_data_conversion/main.py,sha256=LWiYiELF_LY1GghQLt37eZS3ZNojmwHWuSnAhe3qbDI,44768
 psdi_data_conversion/security.py,sha256=wjdrMre29TpkF2NqrsXJ5sschSAnDzqLYTLUcNR21Qw,902
@@ -17,7 +17,7 @@ psdi_data_conversion/bin/mac/atomsk,sha256=pqExRdkR8NSqSasHZjE74R_CiM6Dkr_yvfyak
 psdi_data_conversion/bin/mac/c2x,sha256=dI-bBoQ6uqc6KMYKJaq0x7ejJgOf_wysTxQA5BrF8AY,2581960
 psdi_data_conversion/converters/__init__.py,sha256=15Ldt06eyZ0bgNPB4qg419U0Zcjt6TUCTzjCBo8EIzM,210
 psdi_data_conversion/converters/atomsk.py,sha256=_V33me1e4HW0-YXvdE-z6PdwtSK2gYV6QZf5d8aPqH4,1523
-psdi_data_conversion/converters/base.py,sha256=0hK9IeC306zvQ1qAWb19eI_m_e6CA8TfuEoWgypimeo,36403
+psdi_data_conversion/converters/base.py,sha256=yGlwQmYcLSKP9DH2reTBGvJ-HhfxjO_dYo6qVX501Zw,36515
 psdi_data_conversion/converters/c2x.py,sha256=jDA84H8Jpz--ajTWNWX6K6oMfOMMbMxkA31-VnGi0gU,2019
 psdi_data_conversion/converters/openbabel.py,sha256=OYppOMfnvxmVgRY5vUkcVokWn-bQSSeG8MOFqN1MCIY,13224
 psdi_data_conversion/gui/__init__.py,sha256=Q52GAaJWfNWGDOAEM_fIfAoivLIgM3krhVTiHFTRixM,125
@@ -82,13 +82,13 @@ psdi_data_conversion/templates/documentation.htm,sha256=BeEPgklJOB9tA6jna0Qp4lwR
 psdi_data_conversion/templates/index.htm,sha256=zY9zihO6adJwLU8bB-iaz0AAsRvg24CNx2gVXJFqNLw,7858
 psdi_data_conversion/templates/report.htm,sha256=bru_5EtKqHtKnQ3JB9HpTdK047zCwd5akTLQr2pGd5c,5612
 psdi_data_conversion/testing/__init__.py,sha256=Xku7drtLTYLLPsd403eC0LIEa_iohVifyeyAITy2w7U,135
-psdi_data_conversion/testing/constants.py,sha256=BtIafruSobZ9cFY0VW5Bu209eiftnN8b3ObouZBrFQU,521
+psdi_data_conversion/testing/constants.py,sha256=uYUp3FIwoXG_mDFgitpv0bD5M3xK5ThVm9fUHooons0,519
 psdi_data_conversion/testing/conversion_callbacks.py,sha256=ATR-_BsYCUN8KyOyUjfdWCELzySxLN5jOI0JyrQnmHQ,18858
 psdi_data_conversion/testing/conversion_test_specs.py,sha256=PFzTZYonQ0PsZBKjcn0Hp-UPbwphT3zRH5v-VdNImmQ,27585
 psdi_data_conversion/testing/gui.py,sha256=ul7ixYANIzmOG2ZNOZmQO6wsHmGHdiBGAlw-KuoN0j8,19085
-psdi_data_conversion/testing/utils.py,sha256=A2CDiGr4Gah1eRvGwFmHt1m0F7RdXOxzCuTyYhcAIR4,26122
-psdi_data_conversion-0.2.1.dist-info/METADATA,sha256=jv8iuV3VSQz_4NzFcG5bvTSzO5Ib7WysLqEWFYQ04NU,48538
-psdi_data_conversion-0.2.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-psdi_data_conversion-0.2.1.dist-info/entry_points.txt,sha256=xL7XTzaPRr2E67WhOD1M1Q-76hB8ausQlnNiHzuZQPA,123
-psdi_data_conversion-0.2.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-psdi_data_conversion-0.2.1.dist-info/RECORD,,
+psdi_data_conversion/testing/utils.py,sha256=uhJQUceaNmpQd3SioFLZVMExMVzO3Ds8V9DD2hqP-mQ,26700
+psdi_data_conversion-0.2.2.dist-info/METADATA,sha256=pIAVKNVVo-_VO3lbTA-MTvuR7t9LvUfHoIj0CD30imw,48538
+psdi_data_conversion-0.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+psdi_data_conversion-0.2.2.dist-info/entry_points.txt,sha256=xL7XTzaPRr2E67WhOD1M1Q-76hB8ausQlnNiHzuZQPA,123
+psdi_data_conversion-0.2.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+psdi_data_conversion-0.2.2.dist-info/RECORD,,