psdi-data-conversion 0.1.6__py3-none-any.whl → 0.2.0__py3-none-any.whl

psdi_data_conversion/testing/conversion_test_specs.py

@@ -228,19 +228,39 @@ Not compatible with the GUI, since the GUI can't forcibly delete files uploaded
 """
 
 l_all_test_specs.append(Spec(name="Failed conversion - bad input file",
-                             filename=["quartz_err.xyz", "cyclopropane_err.mol"],
-                             to_format=["inchi", "xyz-0"],
-                             from_format=[None, "mol-0"],
-                             expect_success=False,
-                             converter_name=[CONVERTER_OB, CONVERTER_C2X],
+                             filename=["quartz_err.xyz", "quartz_err.xyz",
+                                       "quartz_err.xyz",
+                                       "cyclopropane_err.mol", "nacl.cif"],
+                             to_format=["inchi", "mol-0",
+                                        "pdb",
+                                        "xyz-0", "bands"],
+                             from_format=[None, None,
+                                          None,
+                                          "mol-0", None],
+                             expect_success=[False, True,
+                                             True,
+                                             False, True],
+                             converter_name=[CONVERTER_OB, CONVERTER_OB,
+                                             CONVERTER_ATO,
+                                             CONVERTER_C2X, CONVERTER_C2X],
                              callback=[MCB(CheckFileStatus(expect_output_exists=False,
                                                            expect_log_exists=None),
                                            CheckException(ex_type=FileConverterAbortException,
                                                           ex_message="Problems reading an XYZ file")),
+                                       MCB(CheckFileStatus(expect_output_exists=True,
+                                                           expect_log_exists=True),
+                                           CheckLogContents("Problems reading an XYZ file: Could not read line #11, "
+                                                            "file error.")),
+                                       MCB(CheckFileStatus(expect_output_exists=True,
+                                                           expect_log_exists=True),
+                                           CheckLogContents("ERROR while trying to read atom #9")),
                                        MCB(CheckFileStatus(expect_output_exists=False,
                                                            expect_log_exists=None),
                                            CheckException(ex_type=FileConverterAbortException,
-                                                          ex_message="Aborting: mol file contains no atoms"))],
+                                                          ex_message="Aborting: mol file contains no atoms")),
+                                       MCB(CheckFileStatus(expect_output_exists=None,
+                                                           expect_log_exists=True),
+                                           CheckLogContents("No eigenvalues to write!"))],
                              ))
 """A test that a conversion that fails due to an unreadable input file will properly fail"""
 

psdi_data_conversion/testing/utils.py

@@ -248,7 +248,7 @@ class SingleConversionTestSpec:
 
     conversion_kwargs: dict[str, Any] = field(default_factory=dict)
     """Any keyword arguments to be provided to the call to `run_converter`, aside from those listed above and
-    `upload_dir` and `download_dir` (for which temporary directories are used)"""
+    `input_dir` and `output_dir` (for which temporary directories are used)"""
 
     expect_success: bool = True
     """Whether or not to expect the test to succeed"""
@@ -333,12 +333,12 @@ def _run_single_test_conversion_with_library(test_spec: SingleConversionTestSpec
 
         exc_info: pytest.ExceptionInfo | None = None
         if test_spec.expect_success:
-            run_converter(filename=qualified_in_filename,
+            run_converter(filename=test_spec.filename,
                           to_format=test_spec.to_format,
                           from_format=test_spec.from_format,
                           name=test_spec.converter_name,
-                          upload_dir=input_dir,
-                          download_dir=output_dir,
+                          input_dir=input_dir,
+                          output_dir=output_dir,
                           **test_spec.conversion_kwargs)
             success = True
         else:
@@ -347,8 +347,8 @@ def _run_single_test_conversion_with_library(test_spec: SingleConversionTestSpec
                               to_format=test_spec.to_format,
                               from_format=test_spec.from_format,
                               name=test_spec.converter_name,
-                              upload_dir=input_dir,
-                              download_dir=output_dir,
+                              input_dir=input_dir,
+                              output_dir=output_dir,
                               **test_spec.conversion_kwargs)
             success = False
 

{psdi_data_conversion-0.1.6.dist-info → psdi_data_conversion-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: psdi_data_conversion
-Version: 0.1.6
+Version: 0.2.0
 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/
@@ -222,8 +222,13 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: File Formats
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.12
+Requires-Dist: igraph
 Requires-Dist: openbabel-wheel
 Requires-Dist: py
+Provides-Extra: deploy
+Requires-Dist: flask; extra == 'deploy'
+Requires-Dist: gunicorn; extra == 'deploy'
+Requires-Dist: requests; extra == 'deploy'
 Provides-Extra: doc
 Requires-Dist: pdoc3; extra == 'doc'
 Provides-Extra: gui
@@ -243,6 +248,9 @@ Description-Content-Type: text/markdown
 
 # PSDI Data Conversion
 
+[![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
 
 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:
@@ -327,7 +335,6 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
 - `LICENSE` (Apache License version 2.0)
 - `pyproject.toml` (Python project metadata and settings)
 - `README.md` (This file)
-- `requirements.txt` (Requirements for the web app deployment of this project)
 
 ## Requirements
 

{psdi_data_conversion-0.1.6.dist-info → psdi_data_conversion-0.2.0.dist-info}/RECORD

@@ -1,12 +1,12 @@
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-psdi_data_conversion/constants.py,sha256=Hq2OVbcSkcv6T87-YJlo1PVlr9ILlB4H3E9JYjzvCF4,7423
-psdi_data_conversion/converter.py,sha256=Y77mqH2OKxf2YelphWDl82AKoRa-APle-l3e8wG_WZA,27315
-psdi_data_conversion/database.py,sha256=XzKvtT-cFmKLWLo5OBB5CV_rGHuqEEuENNyZnbS39qE,56419
+psdi_data_conversion/app.py,sha256=VmZlIAZ_J9W6p_WUcTA_2UNmZxssmq1aT72I2d1ObDc,3606
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 psdi_data_conversion/dist.py,sha256=LOcKEP7H7JA9teX1m-5awuBi69gmdhtUit7yxtCTOZ8,2293
 psdi_data_conversion/file_io.py,sha256=LvdPmnYL_7Xlcr-7LJjUbbky4gKiqTTvPRzdbtvQaJo,8794
 psdi_data_conversion/log_utility.py,sha256=CHAq-JvBnTKaE0SHK5hM5j2dTbfSli4iUc3hsf6dBhc,8789
-psdi_data_conversion/main.py,sha256=9Gu3CxbUfMuDxyNBx_-kQwWB4eOTWRHGmxCsVnpdbvs,42421
+psdi_data_conversion/main.py,sha256=LWiYiELF_LY1GghQLt37eZS3ZNojmwHWuSnAhe3qbDI,44768
 psdi_data_conversion/security.py,sha256=wjdrMre29TpkF2NqrsXJ5sschSAnDzqLYTLUcNR21Qw,902
 psdi_data_conversion/utils.py,sha256=iTjNfrD4n_hU9h20ldYrX2Bmp5KhCBIeMSUMLtPZ_8k,402
 psdi_data_conversion/bin/LICENSE_ATOMSK,sha256=-Ay6SFTAf9x-OaRAiOgMNoutfUMLHx5jQQA1HqZ6p7I,34886
@@ -17,25 +17,28 @@ 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
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 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
+psdi_data_conversion/gui/accessibility.py,sha256=XQyAAJZQdIyRftfidhhVgsZXVtA9b9qZhwwFm899kbE,1302
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 psdi_data_conversion/static/data/data.json,sha256=1nljosxtwbLRfIIIa6-GHJnhvzhB759oEGvVQ18QP_4,3647095
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psdi_data_conversion/static/content/accessibility.htm

@@ -1,255 +0,0 @@
-<!--
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-  Version 1.0, 7th June 2024
--->
-
-<!DOCTYPE html>
-<html>
-
-<head>
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  <title>PSDI Data Conversion Service</title>
-  <link rel="icon" type="image/x-icon" href="../img/psdi-icon-dark.svg">
-  <link href="https://fonts.googleapis.com/css?family=Lato:400" rel="stylesheet" type="text/css">
-  <link href="https://fonts.googleapis.com/css?family=Open+Sans+Condensed:700" rel="stylesheet" type="text/css">
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-  <link rel="stylesheet" href="../styles/format.css">
-
-  <script src="https://code.jquery.com/jquery-3.7.1.js" integrity="sha256-eKhayi8LEQwp4NKxN+CfCh+3qOVUtJn3QNZ0TciWLP4="
-    crossorigin="anonymous"></script>
-
-  <script src="../javascript/load_accessibility.js"></script>
-  <script src="../javascript/common.js" type="module"></script>
-  <script src="../javascript/psdi-common.js" type="module"></script>
-  <script src="../javascript/accessibility.js" type="module" language="JavaScript"></script>
-</head>
-
-<body marginwidth="0">
-
-  <!-- Cover to hide element loading and make page transitions seem smoother -->
-  <div id="cover"></div>
-
-  <header class="header" id="psdi-header"></header>
-
-  <div class="hero">
-    <div class="max-width-box">
-      <h1 class="hero__title marginless_header">Accessibility</h1>
-    </div>
-  </div>
-
-  <form name="gui">
-    <div class="max-width-box">
-      <p>Select accessibility settings below as required, in any order. Each new setting immediately comes into effect
-        on this page only, in the first instance. Once the appearance of the page is satisfactory, clicking on the
-        'Apply' button applies the settings to the entire website. Leaving the page without clicking on 'Apply' results
-        in the changes being lost. Note that page appearance may vary slightly according to the browser used.</p>
-      <p>The colour options here are not compatible with the dark-mode toggle in the header bar. If a custom dark scheme
-        is desired, the appropriate colours can be selected in light-mode.</p>
-      <div class="access-options">
-        <div class="access-option-container">
-          <p>
-            <label for="font" id="fontLabel">Font:</label><br>
-            <select id="font">
-              <option value="Default">Default</option>
-              <option value="Arial" style="font-family: Arial, 'Helvetica Neue', Helvetica, sans-serif;">Arial</option>
-              <option value="Calibri"
-                style="font-family: Calibri, Candara, Segoe, 'Segoe UI', Optima, Arial, sans-serif;">Calibri</option>
-              <option value="Comic Sans" style="font-family: 'Comic Sans MS', 'Comic Sans', sans-serif;">Comic Sans
-              </option>
-              <option value="Courier New"
-                style="font-family: 'Courier New', Courier, 'Lucida Sans Typewriter', 'Lucida Typewriter', monospace;">
-                Courier New</option>
-              <option value="Georgia" style="font-family: Georgia, Times, 'Times New Roman', serif">Georgia
-              </option>
-              <option value="Helvetica" style="font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif">Helvetica
-              </option>
-              <option value="Lexend" style="font-family: Lexend, sans-serif;">Lexend</option>
-              <option value="Lucida Bright" style="font-family: 'Lucida Bright', Georgia, serif">Lucida Bright
-              </option>
-              <option value="Open Sans" style="font-family: Open Sans, sans-serif;">Open Sans
-              </option>
-              <option value="Tahoma" style="font-family: Tahoma, Verdana, Segoe, sans-serif;">Tahoma</option>
-              <option value="Times New Roman"
-                style="font-family: TimesNewRoman, 'Times New Roman', Times, Baskerville, Georgia, serif;">Times New
-                Roman</option>
-              <option value="Trebuchet"
-                style="font-family: 'Trebuchet MS', 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', Tahoma, sans-serif;">
-                Trebuchet</option>
-              <option value="Verdana" style="font-family: Verdana, Geneva, sans-serif;">Verdana</option>
-            </select><br>
-          </p>
-        </div>
-        <div class="access-option-container">
-          <p>
-            <label for="size" id="sizeLabel">Font size (px):</label><br>
-            <select id="size">
-              <option value="Default">Default</option>
-              <option value="14" style="font-size: 14px;">14</option>
-              <option value="15" style="font-size: 15px;">15</option>
-              <option value="16" style="font-size: 16px;">16</option>
-              <option value="17" style="font-size: 17px;">17</option>
-              <option value="18" style="font-size: 18px;">18</option>
-              <option value="19" style="font-size: 19px;">19</option>
-              <option value="20" style="font-size: 20px;">20</option>
-              <option value="21" style="font-size: 21px;">21</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container">
-          <p>
-            <label for="weight" id="weightLabel">Font weight:</label><br>
-            <select id="weight">
-              <option value="Default" style="font-weight: normal;">Default</option>
-              <option value="Bold" style="font-weight: bold;">Bold</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container">
-          <p>
-            <label for="letter" id="letterLabel">Letter spacing (px):</label><br>
-            <select id="letter">
-              <!-- Limitations of how the select element works prevent us from showing a preview of this element
-               in the dropdown -->
-              <option value="Default">Default</option>
-              <option value="0.5">0.5</option>
-              <option value="1.0">1.0</option>
-              <option value="1.5">1.5</option>
-              <option value="2.0">2.0</option>
-              <option value="2.5">2.5</option>
-              <option value="3.0">3.0</option>
-              <option value="3.5">3.5</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container">
-          <p>
-            <label for="line" id="lineLabel">Line spacing:</label><br>
-            <select id="line">
-              <!-- Limitations of how the select element works prevent us from showing a preview of this element
-               in the dropdown -->
-              <option value="Default">Default</option>
-              <option value="1.0">1.0</option>
-              <option value="1.1">1.1</option>
-              <option value="1.2">1.2</option>
-              <option value="1.3">1.3</option>
-              <option value="1.4">1.4</option>
-              <option value="1.5">1.5</option>
-              <option value="1.6">1.6</option>
-              <option value="1.7">1.7</option>
-              <option value="1.8">1.8</option>
-              <option value="1.9">1.9</option>
-              <option value="2.0">2.0</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container lm-only">
-          <p>
-            <label for="dark-colour" id="colourLabel">Primary font colour:</label><br>
-            <select id="dark-colour">
-              <option value="Default">Default</option>
-              <option value="White" style="color: White">White</option>
-              <option value="LightGrey" style="color: LightGrey">LightGrey</option>
-              <option value="DarkGrey" style="color: DarkGrey">DarkGrey</option>
-              <option value="Black" style="color: Black">Black</option>
-              <option value="LightBlue" style="color: LightBlue">LightBlue</option>
-              <option value="Blue" style="color: Blue">Blue</option>
-              <option value="DarkBlue" style="color: DarkBlue">DarkBlue</option>
-              <option value="Purple" style="color: Purple">Purple</option>
-              <option value="Pink" style="color: Pink">Pink</option>
-              <option value="Red" style="color: Red">Red</option>
-              <option value="DarkRed" style="color: DarkRed">DarkRed</option>
-              <option value="Orange" style="color: Orange">Orange</option>
-              <option value="Brown" style="color: Brown">Brown</option>
-              <option value="LightGreen" style="color: LightGreen">LightGreen</option>
-              <option value="Green" style="color: Green">Green</option>
-              <option value="DarkGreen" style="color: DarkGreen">DarkGreen</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container lm-only">
-          <p>
-            <label for="light-colour" id="lightColourLabel">Alternate font colour:</label><br>
-            <select id="light-colour">
-              <option value="Default">Default</option>
-              <option value="White" style="color: White">White</option>
-              <option value="LightGrey" style="color: LightGrey">LightGrey</option>
-              <option value="DarkGrey" style="color: DarkGrey">DarkGrey</option>
-              <option value="Black" style="color: Black">Black</option>
-              <option value="LightBlue" style="color: LightBlue">LightBlue</option>
-              <option value="Blue" style="color: Blue">Blue</option>
-              <option value="DarkBlue" style="color: DarkBlue">DarkBlue</option>
-              <option value="Purple" style="color: Purple">Purple</option>
-              <option value="Pink" style="color: Pink">Pink</option>
-              <option value="Red" style="color: Red">Red</option>
-              <option value="DarkRed" style="color: DarkRed">DarkRed</option>
-              <option value="Orange" style="color: Orange">Orange</option>
-              <option value="Brown" style="color: Brown">Brown</option>
-              <option value="LightGreen" style="color: LightGreen">LightGreen</option>
-              <option value="Green" style="color: Green">Green</option>
-              <option value="DarkGreen" style="color: DarkGreen">DarkGreen</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container lm-only">
-          <p>
-            <label for="lightBackground" id="lightBackgroundLabel">Primary background colour:</label><br>
-            <select id="light-background">
-              <option value="Default">Default</option>
-              <option value="White" style="background-color: White">White</option>
-              <option value="LightGrey" style="background-color: LightGrey">LightGrey</option>
-              <option value="DarkGrey" style="background-color: DarkGrey">DarkGrey</option>
-              <option value="Black" style="background-color: Black">Black</option>
-              <option value="LightBlue" style="background-color: LightBlue">LightBlue</option>
-              <option value="Blue" style="background-color: Blue">Blue</option>
-              <option value="DarkBlue" style="background-color: DarkBlue">DarkBlue</option>
-              <option value="Purple" style="background-color: Purple">Purple</option>
-              <option value="Pink" style="background-color: Pink">Pink</option>
-              <option value="Red" style="background-color: Red">Red</option>
-              <option value="DarkRed" style="background-color: DarkRed">DarkRed</option>
-              <option value="Orange" style="background-color: Orange">Orange</option>
-              <option value="Brown" style="background-color: Brown">Brown</option>
-              <option value="LightGreen" style="background-color: LightGreen">LightGreen</option>
-              <option value="Green" style="background-color: Green">Green</option>
-              <option value="DarkGreen" style="background-color: DarkGreen">DarkGreen</option>
-            </select>
-          </p>
-        </div>
-        <div class="access-option-container lm-only">
-          <p>
-            <label for="darkBackground" id="darkBackgroundLabel">Alternate background colour:</label><br>
-            <select id="dark-background">
-              <option value="Default">Default</option>
-              <option value="White" style="background-color: White">White</option>
-              <option value="LightGrey" style="background-color: LightGrey">LightGrey</option>
-              <option value="DarkGrey" style="background-color: DarkGrey">DarkGrey</option>
-              <option value="Black" style="background-color: Black">Black</option>
-              <option value="LightBlue" style="background-color: LightBlue">LightBlue</option>
-              <option value="Blue" style="background-color: Blue">Blue</option>
-              <option value="DarkBlue" style="background-color: DarkBlue">DarkBlue</option>
-              <option value="Purple" style="background-color: Purple">Purple</option>
-              <option value="Pink" style="background-color: Pink">Pink</option>
-              <option value="Red" style="background-color: Red">Red</option>
-              <option value="DarkRed" style="background-color: DarkRed">DarkRed</option>
-              <option value="Orange" style="background-color: Orange">Orange</option>
-              <option value="Brown" style="background-color: Brown">Brown</option>
-              <option value="LightGreen" style="background-color: LightGreen">Green</option>
-              <option value="Green" style="background-color: Green">Green</option>
-              <option value="DarkGreen" style="background-color: DarkGreen">DarkGreen</option>
-            </select>
-          </p>
-        </div>
-      </div>
-      <input type="button" class="button" value=" Reset " name="resetButton" id="resetButton">
-      <br><span>Apply chosen settings to the entire website:</span>
-      <input type="button" class="button" value=" Apply " name="applyButton" id="applyButton">
-      <div class="medGap"></div>
-
-    </div>
-  </form>
-
-  <footer class="footer" id="psdi-footer"></footer>
-
-</body>
-
-</html>