psdi-data-conversion 0.0.35__py3-none-any.whl → 0.0.36__py3-none-any.whl

psdi_data_conversion/testing/utils.py

@@ -102,13 +102,16 @@ class ConversionTestSpec:
     (as if using zip on the multiple lists) to test each element in turn.
     """
 
+    name: str
+    """The name of this test specification"""
+
     filename: str | Iterable[str] = "nacl.cif"
     """The name of the input file, relative to the input test data location, or a list thereof"""
 
     to_format: str | Iterable[str] = "pdb"
     """The format to test converting the input file to, or a list thereof"""
 
-    name: str | Iterable[str] = CONVERTER_DEFAULT
+    converter_name: str | Iterable[str] = CONVERTER_DEFAULT
     """The name of the converter to be used for the test, or a list thereof"""
 
     conversion_kwargs: dict[str, Any] | Iterable[dict[str, Any]] = field(default_factory=dict)
@@ -124,6 +127,15 @@ class ConversionTestSpec:
     should take as its only argument a `ConversionTestInfo` and return a string. The string should be empty if the check
     is passed and should explain the failure otherwise."""
 
+    compatible_with_library: bool = True
+    """Whether or not this test spec is compatible with being run through the Python library, default True"""
+
+    compatible_with_cla: bool = True
+    """Whether or not this test spec is compatible with being run through the command-line application, default True"""
+
+    compatible_with_gui: bool = True
+    """Whether or not this test spec is compatible with being run through the GUI, default True"""
+
     def __post_init__(self):
         """Regularize the lengths of all attribute lists, in case some were provided as single values and others as
         lists, and set up initial values
@@ -131,7 +143,10 @@ class ConversionTestSpec:
 
         # To ease maintainability, we get the list of this class's attributes automatically from its __dict__, excluding
         # any which start with an underscore
-        self._l_attr_names: list[str] = [attr_name for attr_name in self.__dict__ if not attr_name.startswith("_")]
+        self._l_attr_names: list[str] = [attr_name for attr_name in self.__dict__ if
+                                         not (attr_name.startswith("_") or
+                                              attr_name == "name" or
+                                              attr_name.startswith("compatible"))]
 
         l_single_val_attrs = []
         self._len: int = 1
@@ -196,7 +211,7 @@ class SingleConversionTestSpec:
     to_format: str
     """The format to test converting the input file to"""
 
-    name: str | Iterable[str] = CONVERTER_DEFAULT
+    converter_name: str | Iterable[str] = CONVERTER_DEFAULT
     """The name of the converter to be used for the test"""
 
     conversion_kwargs: dict[str, Any] = field(default_factory=dict)
@@ -279,7 +294,7 @@ def _run_single_test_conversion_with_library(test_spec: SingleConversionTestSpec
         if test_spec.expect_success:
             run_converter(filename=qualified_in_filename,
                           to_format=test_spec.to_format,
-                          name=test_spec.name,
+                          name=test_spec.converter_name,
                           upload_dir=input_dir,
                           download_dir=output_dir,
                           **test_spec.conversion_kwargs)
@@ -288,7 +303,7 @@ def _run_single_test_conversion_with_library(test_spec: SingleConversionTestSpec
             with pytest.raises(Exception) as exc_info:
                 run_converter(filename=qualified_in_filename,
                               to_format=test_spec.to_format,
-                              name=test_spec.name,
+                              name=test_spec.converter_name,
                               upload_dir=input_dir,
                               download_dir=output_dir,
                               **test_spec.conversion_kwargs)
@@ -359,7 +374,7 @@ def _run_single_test_conversion_with_cla(test_spec: SingleConversionTestSpec,
         if test_spec.expect_success:
             run_converter_through_cla(filename=qualified_in_filename,
                                       to_format=test_spec.to_format,
-                                      name=test_spec.name,
+                                      name=test_spec.converter_name,
                                       input_dir=input_dir,
                                       output_dir=output_dir,
                                       log_file=os.path.join(output_dir, test_spec.log_filename),
@@ -369,7 +384,7 @@ def _run_single_test_conversion_with_cla(test_spec: SingleConversionTestSpec,
             with pytest.raises(SystemExit) as exc_info:
                 run_converter_through_cla(filename=qualified_in_filename,
                                           to_format=test_spec.to_format,
-                                          name=test_spec.name,
+                                          name=test_spec.converter_name,
                                           input_dir=input_dir,
                                           output_dir=output_dir,
                                           log_file=os.path.join(output_dir, test_spec.log_filename),

{psdi_data_conversion-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: psdi_data_conversion
-Version: 0.0.35
+Version: 0.0.36
 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/
@@ -403,13 +403,21 @@ In addition to the dependencies listed above, this project uses the assets made
 
 ### Installation
 
-The CLA and Python library are installed together. This package is not yet available on PyPI, and so must be installed locally. This can be done most easily with:
+The CLA and Python library are installed together. This project is available on PyPI, and so can be installed via pip with:
+
+```bash
+pip install psdi-data-conversion
+```
+
+If you wish to install from source, this can be done most easily by cloning the project and then executing:
 
 ```bash
 pip install .
 ```
 
-executed from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
+from this project's directory. You can also replace the '.' in this command with the path to this project's directory to install it from elsewhere.
+
+**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
 
 Depending on your system, it may not be possible to install packages in this manner without creating a virtual environment to do so in. You can do this by first installing the `venv` module for Python3 with e.g.:
 
@@ -572,15 +580,23 @@ Enter https://data-conversion.psdi.ac.uk/ in a browser. Guidance on usage is giv
 
 ### Installation and Setup
 
-Install the package and its requirements, including the optional requirements used to run the GUI locally, by executing the following command from this project's directory:
+This project is available on PyPI, and so can be installed via pip, including the necessary dependencies for the GUI, with:
+
+```bash
+pip install psdi-data-conversion'[gui]'
+```
+
+If you wish to install the project locally from source, this can be done most easily by cloning the project and then executing:
 
 ```bash
 pip install .'[gui]'
 ```
 
-If your system does not allow installs in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
+**Note:** This project uses git to determine the version number. If you clone the repository, you won't have to do anything special here, but if you get the source e.g. by extracting a release archive, you'll have to do one additional step before running the command above. If you have git installed, simply run `git init` in the project directory and it will be able to install. Otherwise, edit the project's `pyproject.toml` file to uncomment the line that sets a fixed version, and comment out the lines that set it up to determine the version from git - these are pointed out in the comments there.
 
-If you've cloned this repository, you can use the `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
+If your system does not allow installation in this manner, it may be necessary to set up a virtual environment. See the instructions in the [command-line application installation](#installation) section above for how to do that, and then try to install again once you've set one up and activated it.
+
+If you've installed this repository from source, you can use the provided `run_local.sh` bash script to run the application. Otherwise (e.g. if you've installed from a wheel or PyPI), copy and paste the following into a script:
 
 ```bash
 #!/bin/bash
@@ -590,6 +606,13 @@ if [ -z $MAX_FILESIZE ]; then
   export MAX_FILESIZE=0
 fi
 
+# The envvar MAX_FILESIZE_OB can be used to set the maximum allowed filesize in MB for the Open Babel converter - 0
+# indicates no maximum. This is currently set to 1 MB by default as the converter seems to hang above this limit (not
+# even allowing the process to be cancelled). This can be changed in the future if this is patched
+if [ -z $MAX_FILESIZE_OB ]; then
+  export MAX_FILESIZE_OB=1
+fi
+
 # Logging control - "full" sets server-style logging, which is necessary to produce the output logs with the expected
 # names. This should not be changed, or else errors will occur
 export LOG_MODE=full

{psdi_data_conversion-0.0.35.dist-info → psdi_data_conversion-0.0.36.dist-info}/RECORD

@@ -1,12 +1,12 @@
 psdi_data_conversion/__init__.py,sha256=urMsTqsTHTch1q4rMT9dgGnrvdPFMP9B8r-6Kr8H5sE,404
-psdi_data_conversion/app.py,sha256=hIJEGiUVkBMjuXFOhk9HEkqV99tWkNSErC7OVmTlDpc,8149
-psdi_data_conversion/constants.py,sha256=JpWqrjcCsLbZBWpiuP8XcR0y6wHT6EDMpiXBQwU-rfY,7274
-psdi_data_conversion/converter.py,sha256=ejGBLYrDTSk2wBEOEYXa3rIHtV7-e1oE96a9JVNEpdE,22196
-psdi_data_conversion/database.py,sha256=QVLWZqLVQvrn1rZvchugfu3kyDroN231_4BwjHOpAOs,44061
+psdi_data_conversion/app.py,sha256=LMVK3R8Ooz0vj8Pb4N5MkKQDOb91i5FhH5aHty5RDDM,8998
+psdi_data_conversion/constants.py,sha256=jh9-EqTt3E5I5H5axpANjQI_JuVeqsACoUVHuw6RX8Y,7351
+psdi_data_conversion/converter.py,sha256=f5Uos26M3KfDFQ-zoEOJVs0lEASkYRQyXrR0B9MhDmU,22906
+psdi_data_conversion/database.py,sha256=WMOdz6T2b2XuE_d-Ex_v5oRi-TDEHcku_yT04en4GoE,44274
 psdi_data_conversion/dist.py,sha256=Ju6BcEuLrB738diTbK6HX6ZBiZ40Ctq1exj44nSCMlE,2292
 psdi_data_conversion/file_io.py,sha256=UXxNxTl_EabQ96UrLp4b38ctkYhXV_KIHJeTuyRBVpM,8857
 psdi_data_conversion/log_utility.py,sha256=WIgQp0pMsFtJJZKgIhStBNnjLzC6gEIodQAoXji5ht0,8789
-psdi_data_conversion/main.py,sha256=I854YMpEgdwchQs0lXqR7U3leoz18U4_QqW7nylt_XE,37857
+psdi_data_conversion/main.py,sha256=90vCObJSG7Xxi_iyx2awskOt8RT9_Erel9rT8uz0n78,38203
 psdi_data_conversion/security.py,sha256=wjdrMre29TpkF2NqrsXJ5sschSAnDzqLYTLUcNR21Qw,902
 psdi_data_conversion/bin/LICENSE_ATOMSK,sha256=-Ay6SFTAf9x-OaRAiOgMNoutfUMLHx5jQQA1HqZ6p7I,34886
 psdi_data_conversion/bin/LICENSE_C2X,sha256=-Ay6SFTAf9x-OaRAiOgMNoutfUMLHx5jQQA1HqZ6p7I,34886
@@ -15,26 +15,26 @@ psdi_data_conversion/bin/linux/c2x,sha256=gi4XsMbJu7lFxckc_FNYmfDf35yZPSToh6Hm5L
 psdi_data_conversion/bin/mac/atomsk,sha256=pqExRdkR8NSqSasHZjE74R_CiM6Dkr_yvfyakdTWtI8,4502371
 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=XaB73EGuxDpJXl4679Egdy9jbnP-O2aO8vMC_D4qd5o,1400
-psdi_data_conversion/converters/base.py,sha256=yG4wqMpxnt-TBs-ACimI60gEdy1d3vhJsn1DjQ6U5BE,32672
-psdi_data_conversion/converters/c2x.py,sha256=bGvh9FDim5KMHtZWblj6BV8NPg1_EVtmiv5zByqEhBE,1375
-psdi_data_conversion/converters/openbabel.py,sha256=L_YN83C3PVpa2r67CKf7RVt_2UY6BpNvQg1jztKF0wM,10305
+psdi_data_conversion/converters/atomsk.py,sha256=_V33me1e4HW0-YXvdE-z6PdwtSK2gYV6QZf5d8aPqH4,1523
+psdi_data_conversion/converters/base.py,sha256=QTXOWEkrKmQvBANEmJilNtI3i0fRFkbVetVtYk8zXxw,35535
+psdi_data_conversion/converters/c2x.py,sha256=RjvOUxrb7R09s58p1kQKhICVUvozNJc4bvhQGkk89Ng,1498
+psdi_data_conversion/converters/openbabel.py,sha256=BGEXPdOfm5QNO67gymH8PrmW88pMvXF8_9fosz3_Bcg,13150
 psdi_data_conversion/scripts/atomsk.sh,sha256=N_NMO5q8sI3Lt1TerC-xcKbMI0kfscAudy5UAbY0uR0,804
 psdi_data_conversion/scripts/c2x.sh,sha256=F48jhgtgouKKZDQ9p6tCCNBN5bPuidBq2GcTurdWzQc,770
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 psdi_data_conversion/static/content/header-links.html,sha256=7B2bHa7dLfSZ4hPMvVJ3kR0niVAOO3FtHJo0K6m1oP4,693
 psdi_data_conversion/static/content/psdi-common-footer.html,sha256=CM9F6AXM1LVMLvTP51xTzOicEelSXlyXQyN-BjrQAJk,3933
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-psdi_data_conversion/static/content/report.htm,sha256=o0Fn6QgKIEr2KtDoucQ203F3YhHQCIbAnbMvU7ylgh8,4530
+psdi_data_conversion/static/content/psdi-common-header.html,sha256=vRAgLGKE_RhXgBUQnarxnpkGl9j2Qeedqqo3VNDVGdk,1825
+psdi_data_conversion/static/content/report.htm,sha256=CRwlF7a7QvAjHsajuehWOtLxbo-JAjqrS_Q-I4BWxzs,4549
 psdi_data_conversion/static/content/index-versions/header-links.html,sha256=WN9oZL7hLtH_yv5PvX3Ky7_YGrNvQL_RQ5eU8DB50Rg,764
 psdi_data_conversion/static/content/index-versions/psdi-common-footer.html,sha256=zzizo_YEPhvH3_jNPFkFoKZA0TnIG6EXzQOsgooU1K8,3989
-psdi_data_conversion/static/content/index-versions/psdi-common-header.html,sha256=FQevMlVaiQ8tRb381El7DYq_9VSNbtpL9EeImDdwDfM,1809
+psdi_data_conversion/static/content/index-versions/psdi-common-header.html,sha256=IXmvdlArY-60b7HgvKjcNF3eSmEmTImX7Hdasswyi5s,1907
 psdi_data_conversion/static/data/data.json,sha256=_3o3BFEmnWGhoGMaviJsu-U9dJnk_tH9Wf0g-eDVWuU,3630027
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@@ -61,26 +61,26 @@ psdi_data_conversion/static/img/ukri-epsr-logo-lighttext.png,sha256=Am-5nHjr-yA_
 psdi_data_conversion/static/img/ukri-logo-darktext.png,sha256=3UgghERAmFdnre0FfcA8JcskVLbnOn-oH4MCWEazyD4,25570
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 psdi_data_conversion/static/javascript/accessibility.js,sha256=kbnWHeBNPrTLrnYRjMEUmiOcCXM2bORYIRfzUB03TAE,7208
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