psdi-data-conversion 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

psdi_data_conversion/constants.py

@@ -151,7 +151,7 @@ QUAL_CONN_LABEL = "Atomic connections are"
 QUAL_2D_KEY = "two_dim"
 QUAL_2D_LABEL = "2D atomic coordinates are"
 QUAL_3D_KEY = "three_dim"
-QUAL_3D_LABEL = "2D atomic coordinates are"
+QUAL_3D_LABEL = "3D atomic coordinates are"
 
 # Notes for conversion quality
 QUAL_NOTE_IN_UNKNOWN = ("Potential data extrapolation: {} represented in the output format but its representation in "

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

@@ -9,12 +9,14 @@ from __future__ import annotations
 
 import json
 import os
+import sys
 from copy import copy
 from dataclasses import dataclass, field
 from functools import lru_cache
 from itertools import product
 from logging import getLogger
 from typing import Any, Literal, overload
+from warnings import catch_warnings
 
 import igraph as ig
 
@@ -22,6 +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
@@ -863,12 +866,18 @@ class ConversionsTable:
             # TODO: When there's some better measure of conversion quality, use it to choose which converter to use
             return [l_possible_direct_conversions[0]]
 
-        # Query the graph for the shortest paths to perform this conversion
         graph: ig.Graph = self._get_desired_graph(only)
-        l_paths: list[list[int]] = graph.get_shortest_paths(in_format_info.id, to=out_format_info.id)
+
+        # Query the graph for the shortest paths to perform this conversion. If no conversions are possible, igraph
+        # will print a warning, which we catch and suppress here
+        with catch_warnings(record=True) as l_warnings:
+            l_paths: list[list[int]] = graph.get_shortest_paths(in_format_info.id, to=out_format_info.id)
+            for warning in l_warnings:
+                if "Couldn't reach some vertices" not in str(warning.message):
+                    print(warning, file=sys.stderr)
 
         # Check if any paths are possible
-        if not l_paths:
+        if not l_paths or not l_paths[0]:
             return None
 
         # Check each path to find the first which doesn't lose any unnecessary info, or else the one which loses the
@@ -1198,10 +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-0.2.0.dist-info → psdi_data_conversion-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: psdi_data_conversion
-Version: 0.2.0
+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/
@@ -241,6 +241,8 @@ Requires-Dist: pytest; extra == 'gui-test'
 Requires-Dist: requests; extra == 'gui-test'
 Requires-Dist: selenium; extra == 'gui-test'
 Requires-Dist: webdriver-manager; extra == 'gui-test'
+Provides-Extra: plots
+Requires-Dist: matplotlib; extra == 'plots'
 Provides-Extra: test
 Requires-Dist: coverage; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
@@ -251,7 +253,7 @@ Description-Content-Type: text/markdown
 [![License Badge](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 ![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/brgillis/dbd938192dc4de9b7779978e515c0e79/raw/covbadge.json)
 
-Release date: 2024-04-29
+Release date: 2024-06-03
 
 This is the repository for the PSDI PF2 Chemistry File Format Conversion project. The goal of this project is to provide utilities to assist in converting files between the many different file formats used in chemistry, providing information on what converters are available for a given conversion and the expected quality of it, and providing multiple interfaces to perform these conversions. These interfaces are:
 

{psdi_data_conversion-0.2.0.dist-info → psdi_data_conversion-0.2.2.dist-info}/RECORD

@@ -1,10 +1,10 @@
 psdi_data_conversion/__init__.py,sha256=urMsTqsTHTch1q4rMT9dgGnrvdPFMP9B8r-6Kr8H5sE,404
 psdi_data_conversion/app.py,sha256=VmZlIAZ_J9W6p_WUcTA_2UNmZxssmq1aT72I2d1ObDc,3606
-psdi_data_conversion/constants.py,sha256=w-P3QrS2MQm3gorqZfKqX15YhOTvqZSZ7h6pdxwlzao,7348
+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=86jxDXNnyo44lUg78IvwmhyoZaNzNCL9crSZbzcokm4,65284
-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-0.2.0.dist-info/METADATA,sha256=_GG0nAM1Dm9QdA5DW9UZVPWf9izJNgwKqj7OeNfy9pU,48472
-psdi_data_conversion-0.2.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-psdi_data_conversion-0.2.0.dist-info/entry_points.txt,sha256=xL7XTzaPRr2E67WhOD1M1Q-76hB8ausQlnNiHzuZQPA,123
-psdi_data_conversion-0.2.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-psdi_data_conversion-0.2.0.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,,