psdi-data-conversion 0.0.36__tar.gz → 0.0.37__tar.gz

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/CONTRIBUTING.md

@@ -297,6 +297,22 @@ For debugging python issues, it's recommended to install the package in editable
 pip install --editable .'[gui-test]'
 ```
 
+### Running Unit Tests
+
+The GUI unit tests require a web driver to be installed, and will install one if one isn't. To avoid repeated unnecessary API calls for the installation, you can set the environmental variable `DRIVER` when running tests to the location of your driver. This can be set to be automatically picked up by many IDEs by setting this in a `.env` file in the root of your project, e.g.:
+
+```
+DRIVER=~/.wdm/drivers/geckodriver/linux64/v0.36.0/geckodriver
+```
+
+To get the address of your driver, you can run the following in a Python terminal from within this projects virtual environment (after installing the `[gui-test]` optional dependencies):
+
+```python
+from webdriver_manager.firefox import GeckoDriverManager
+driver_path = GeckoDriverManager().install()
+print(f"Gecko driver installed to: {driver_path}")
+```
+
 ## Continuous Integration
 
 This project uses various GitHub workflows to perform Continuous Integration tasks. These can be found in the `.github/workflows` folder. The files which start with "ci-" are the directly-triggered workflows, and the files which start with "job-" are reusable workflows called by the former. These workflows handle the following tasks:
@@ -310,7 +326,7 @@ See the commons within the files for further details.
 
 ## Publishing
 
-The Python library, CLA, and local GUI are (planned to be) published as a Python package via PyPI. This section describes how the package is set up and how it's published.
+The Python library, CLA, and local GUI are published as a Python package via PyPI. This section describes how the package is set up and how it's published.
 
 ### Package Setup
 
@@ -318,11 +334,11 @@ The package's setup is defined in the `pyproject.toml` file. This defines the pr
 
 The package uses [Hatch](https://hatch.pypa.io/latest/) for its build backend, as it is simpler to configure than the classic [Setuptools](https://setuptools.pypa.io/en/latest/userguide/) and provides some useful extensibility.
 
-The version of the package is set to be determined from the version control system, meaning on the release branch, the version will always match the latest tag.
+The version of the package is set to be determined from the version control system, meaning on the release branch, the version will always match the latest tag. This alleviates us of having to manually maintain the version for the package to keep it correct, but does result in some quirks. It's a bit fussier to set up (though that's done now), and it makes the user take an extra step if they want to install from source but haven't cloned the repository - this is noted in the installation instructions in the README.
 
 ### Initial Publication
 
-This section details the plan for the initial publication of this package - after this is complete, this section will be left in for reference in case of future need.
+This section details the proceduce for the initial publication of this package - now that this is complete, this section is left in for reference in case of future need.
 
 First, it's necessary to install a couple required packages in order to build a Python package: `build` to build it and `twine` to upload it. These can be installed with pip via:
 
@@ -350,6 +366,14 @@ To upload, follow [this tutorial](https://packaging.python.org/en/latest/tutoria
 
 The `ci-release.yml` workflow is planned to publish any new releases to PyPI after the initial publication. This can be set up by uncommenting the relevant lines in this file, possibly updating the `job-publish-pypi.yml` to enable this (testing will be necessary), and setting up Trusted Publishing for the project on PyPI (see [guide](https://docs.github.com/en/actions/security-for-github-actions/security-hardening-your-deployments/configuring-openid-connect-in-pypi))
 
+### Project Management
+
+This project is published on PyPI at https://pypi.org/project/psdi-data-conversion/ and on TestPyPI at https://test.pypi.org/project/psdi-data-conversion/. Maintainers can manage the project through the "Manage" link on that page or from their own projects page.
+
+The most important setting to be aware of here is Publishing -> Trusted Publisher Management. This is the system used to allow automatic publishing of releases from GitHub. It's set up so that the current project, organisation, environment, and workflow for publishing are approved. If any of these change, this will need to be updated by adding a new trusted publisher with the new settings (on both PyPI and TestPyPI) and removing the old one.
+
+The management page can also be used to add or remove collaborators through the Collaborators tab. Generally the project on these sites doesn't require much maintenance, but at least a few active collaborators should be on it at all times to avoid getting locked out if someone is suddenly unavailable.
+
 ## Deployment
 
 Deployment is handled by the `job-deploy-k8s.yml` reusable workflow, which is triggered from `ci-main.yml` to deploy to dev on each push to `main` and `ci-release.yml` to deploy to staging on each push to `release`. When a push to production is desired, it must be triggered manually by calling the `ci-deploy-production.yml` workflow on the `release` branch (it's set up to fail if run on any other branch).

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: psdi_data_conversion
-Version: 0.0.36
+Version: 0.0.37
 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/
@@ -278,7 +278,10 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
   - [Installation and Setup](#installation-and-setup)
   - [Running the App](#running-the-app)
 - [Testing](#testing)
-- [Licencing](#licencing)
+- [Troubleshooting](#troubleshooting)
+  - [OSError: [Errno 24] Too many open files](#oserror-errno-24-too-many-open-files)
+  - [Errors running c2x or Atomsk converters](#errors-running-c2x-or-atomsk-converters)
+- [Licensing](#licensing)
 - [Contributors](#contributors)
 - [Funding](#funding)
 
@@ -312,15 +315,17 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
 - `test_data`
   - (Files used for testing the project)
 - `tests`
-  - (Unit tests for the project)
+  - `gui`
+    - (Unit tests for the GUI, aka the local version of the web app)
+  - `python`
+    - (Unit tests for the Python library and command-line application)
 - `CHANGELOG.md` (Updates since initial public release)
 - `CONTRIBUTING.md` (Guidelines and information for contributors to the project)
 - `DOCKERFILE` (Dockerfile for image containerising PSDI's data conversion service)
-- `LICENSE` (Apache Licence version 2.0)
+- `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)
-- `run_local.sh` (Helper script to run the web app locally)
 
 ## Requirements
 
@@ -596,50 +601,9 @@ pip install .'[gui]'
 
 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
-
-# The envvar MAX_FILESIZE can be used to set the maximum allowed filesize in MB - 0 indicates no maximum
-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
-
-# The level to log at. Leave blank for defaults, which logs at INFO level for user output and ERROR level for the server
-# log and stdout. If set to a different value here (e.g. DEBUG), all these channels will be set to that level
-export LOG_LEVEL=
-
-# The envvar SERVICE_MODE can be set to "true" to make this behave as if it's running as the public web service -
-# uncomment the following line to enable that
-# export SERVICE_MODE=true
-
-# Uncomment the following line to enable debug mode
-# export FLASK_ENV=development
-
-# Execute a local run of the application from the proper path
-
-PACKAGE_PATH=`python -c "import psdi_data_conversion; print(psdi_data_conversion.__path__[0])"`
-cd $PACKAGE_PATH/..
-python -m flask --app psdi_data_conversion/app.py run
-```
-
-If desired, you can modify the environmental variables set in this script to modify the operation - see the comments on each for details.
-
 ### Running the App
 
-Run the `run_local.sh` script to start the server. You can then access the website by going to <http://127.0.0.1:5000> in a browser (this will also be printed in the terminal, and you can CTRL+click it there to open it in your default browser). Guidance for using the app is given on each page of it.
+Once installed, the command-line script `psdi-data-convert-gui` will be made available, which can be called to start the server. You can then access the website by going to <http://127.0.0.1:5000> in a browser (this will also be printed in the terminal, and you can CTRL+click it there to open it in your default browser). Guidance for using the app is given on each page of it. When you're finished with the app, key CTRL+C in the terminal where you called the script to shut down the server, or, if the process was backgrounded, kill the appropriate process.
 
 In case of problems when using Chrome, try opening Chrome from the command line:
 open -a "Google Chrome.app" --args --allow-file-access-from-files
@@ -662,28 +626,80 @@ To test the CLA and Python library, install the optional testing requirements lo
 
 ```bash
 pip install .'[test]'
-pytest
+pytest tests/python
 ```
 
 To test the local version of the web app, install the GUI testing requirements locally (which also include the standard GUI requirements and standard testing requirements), start the server, and test by executing the GUI test script:
 
 ```bash
 pip install .'[gui-test]'
-./run_local.sh & # Start the server for the web app in the background
-cd tests/selenium
-./run.sh
-kill %1 # Stop the web server - it may have a different job ID. If you don't know the job ID, you can alternatively call "fg" to bring the job to the foreground, then type CTRL+c to stop it
+pytest tests/gui
+```
+
+Both of these sets of tests can also be run together if desired through:
+
+```bash
+pip install .'[gui-test]'
+pytest
 ```
 
-## Licencing
+## Troubleshooting
+
+This section presents solutions for commonly-encountered issues.
+
+### OSError: [Errno 24] Too many open files
+
+You may see the error:
+
+```
+OSError: [Errno 24] Too many open files
+```
+
+while running the command-line application, using the Python library, or running tests This error is caused by a program hitting the limit of the number of open filehandles allowed by the OS. This limit is typically set to 1024 on Linux systems and 256 on MacOS systems, and thus this issue occurs much more often on the latter. You can see what your current limit is by running the command:
+
+```bash
+ulimit -a | grep "open files"
+```
+
+This limit can be temporarily increased for the current terminal session by running the command:
+
+```bash
+ulimit -n 1024 # Or another, higher number
+```
+
+First, try increasing the limit and then redo the operation which caused this error to see if this resolves it. If this does, you can make this change permanent in a few ways, the easiest of which is to add this command to your `.bashrc` file so it will be set for every new terminal session.
+
+If you see this error when the filehandle limit is already set to a high value such as 1024, this may indicate the presence of a bug in the project which causes a leaking of filehandles, so please open an issue about it, pasting the error you get and the details of your system, particularly including your current filehandle limit.
+
+### Errors running c2x or Atomsk converters
+
+We provide support for the c2x and Atomsk converters by packing binaries which support common Linux and MacOS platforms with this project, but we cannot guarantee universal support for these binaries. In particular, they may rely on dynamically-linked libraries which aren't installed on your system.
+
+Look through the error message you received for messages such as "Library not loaded" or "no such file", and see if they point to the name of a library which you can try installing. For instance, if you see that it's searching for `libquadmath.0.dylib` but not finding it, you can try installing this library. In this case, this library can be installed through apt with:
+
+```bash
+sudo apt install libquadmath0
+```
+
+or through brew via:
+
+```bash
+brew install gcc
+```
+
+Alternatively, you can run your own versions of the `c2x` and `atomsk` binaries with this project. Compile them yourself however you wish - see the projects at https://github.com/codenrx/c2x and https://github.com/pierrehirel/atomsk and follow their instructions to build a binary on your system. Once you've done so, add the binary to your `$PATH`, and this project will pick that up and use it in preference to the prepackaged binary.
+
+On the other hand, it's possible that an error of this sort will occur if you have a non-working binary of one of these converters in your `$PATH`. If this might be the case, you can try removing it and see if the prepackaged binary works for you, or else recompile it to try to fix errors.
+
+## Licensing
 
 This project is provided under the Apache License version 2.0, the terms of which can be found in the file `LICENSE`.
 
-This project redistributes compiled binaries for the Atomsk and c2x converters. These are both licenced under the
+This project redistributes compiled binaries for the Atomsk and c2x converters. These are both licensed under the
 GNU General Public License version 3 and are redistributed per its terms. Any further redistribution of these binaries,
-including redistribution of this project as a whole, including them, must also follow the terms of this licence.
+including redistribution of this project as a whole, including them, must also follow the terms of this license.
 
-This requires conspicuously displaying notice of this licence, providing the text of of the licence (provided here in
+This requires conspicuously displaying notice of this license, providing the text of of the license (provided here in
 the files `psdi_data_conversion/bin/LICENSE_C2X` and `psdi_data_conversion/bin/LICENSE_ATOMSK`), and appropriately
 conveying the source code for each of these. Their respective source code may be found at:
 

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/README.md

@@ -33,7 +33,10 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
   - [Installation and Setup](#installation-and-setup)
   - [Running the App](#running-the-app)
 - [Testing](#testing)
-- [Licencing](#licencing)
+- [Troubleshooting](#troubleshooting)
+  - [OSError: [Errno 24] Too many open files](#oserror-errno-24-too-many-open-files)
+  - [Errors running c2x or Atomsk converters](#errors-running-c2x-or-atomsk-converters)
+- [Licensing](#licensing)
 - [Contributors](#contributors)
 - [Funding](#funding)
 
@@ -67,15 +70,17 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
 - `test_data`
   - (Files used for testing the project)
 - `tests`
-  - (Unit tests for the project)
+  - `gui`
+    - (Unit tests for the GUI, aka the local version of the web app)
+  - `python`
+    - (Unit tests for the Python library and command-line application)
 - `CHANGELOG.md` (Updates since initial public release)
 - `CONTRIBUTING.md` (Guidelines and information for contributors to the project)
 - `DOCKERFILE` (Dockerfile for image containerising PSDI's data conversion service)
-- `LICENSE` (Apache Licence version 2.0)
+- `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)
-- `run_local.sh` (Helper script to run the web app locally)
 
 ## Requirements
 
@@ -351,50 +356,9 @@ pip install .'[gui]'
 
 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
-
-# The envvar MAX_FILESIZE can be used to set the maximum allowed filesize in MB - 0 indicates no maximum
-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
-
-# The level to log at. Leave blank for defaults, which logs at INFO level for user output and ERROR level for the server
-# log and stdout. If set to a different value here (e.g. DEBUG), all these channels will be set to that level
-export LOG_LEVEL=
-
-# The envvar SERVICE_MODE can be set to "true" to make this behave as if it's running as the public web service -
-# uncomment the following line to enable that
-# export SERVICE_MODE=true
-
-# Uncomment the following line to enable debug mode
-# export FLASK_ENV=development
-
-# Execute a local run of the application from the proper path
-
-PACKAGE_PATH=`python -c "import psdi_data_conversion; print(psdi_data_conversion.__path__[0])"`
-cd $PACKAGE_PATH/..
-python -m flask --app psdi_data_conversion/app.py run
-```
-
-If desired, you can modify the environmental variables set in this script to modify the operation - see the comments on each for details.
-
 ### Running the App
 
-Run the `run_local.sh` script to start the server. You can then access the website by going to <http://127.0.0.1:5000> in a browser (this will also be printed in the terminal, and you can CTRL+click it there to open it in your default browser). Guidance for using the app is given on each page of it.
+Once installed, the command-line script `psdi-data-convert-gui` will be made available, which can be called to start the server. You can then access the website by going to <http://127.0.0.1:5000> in a browser (this will also be printed in the terminal, and you can CTRL+click it there to open it in your default browser). Guidance for using the app is given on each page of it. When you're finished with the app, key CTRL+C in the terminal where you called the script to shut down the server, or, if the process was backgrounded, kill the appropriate process.
 
 In case of problems when using Chrome, try opening Chrome from the command line:
 open -a "Google Chrome.app" --args --allow-file-access-from-files
@@ -417,28 +381,80 @@ To test the CLA and Python library, install the optional testing requirements lo
 
 ```bash
 pip install .'[test]'
-pytest
+pytest tests/python
 ```
 
 To test the local version of the web app, install the GUI testing requirements locally (which also include the standard GUI requirements and standard testing requirements), start the server, and test by executing the GUI test script:
 
 ```bash
 pip install .'[gui-test]'
-./run_local.sh & # Start the server for the web app in the background
-cd tests/selenium
-./run.sh
-kill %1 # Stop the web server - it may have a different job ID. If you don't know the job ID, you can alternatively call "fg" to bring the job to the foreground, then type CTRL+c to stop it
+pytest tests/gui
+```
+
+Both of these sets of tests can also be run together if desired through:
+
+```bash
+pip install .'[gui-test]'
+pytest
 ```
 
-## Licencing
+## Troubleshooting
+
+This section presents solutions for commonly-encountered issues.
+
+### OSError: [Errno 24] Too many open files
+
+You may see the error:
+
+```
+OSError: [Errno 24] Too many open files
+```
+
+while running the command-line application, using the Python library, or running tests This error is caused by a program hitting the limit of the number of open filehandles allowed by the OS. This limit is typically set to 1024 on Linux systems and 256 on MacOS systems, and thus this issue occurs much more often on the latter. You can see what your current limit is by running the command:
+
+```bash
+ulimit -a | grep "open files"
+```
+
+This limit can be temporarily increased for the current terminal session by running the command:
+
+```bash
+ulimit -n 1024 # Or another, higher number
+```
+
+First, try increasing the limit and then redo the operation which caused this error to see if this resolves it. If this does, you can make this change permanent in a few ways, the easiest of which is to add this command to your `.bashrc` file so it will be set for every new terminal session.
+
+If you see this error when the filehandle limit is already set to a high value such as 1024, this may indicate the presence of a bug in the project which causes a leaking of filehandles, so please open an issue about it, pasting the error you get and the details of your system, particularly including your current filehandle limit.
+
+### Errors running c2x or Atomsk converters
+
+We provide support for the c2x and Atomsk converters by packing binaries which support common Linux and MacOS platforms with this project, but we cannot guarantee universal support for these binaries. In particular, they may rely on dynamically-linked libraries which aren't installed on your system.
+
+Look through the error message you received for messages such as "Library not loaded" or "no such file", and see if they point to the name of a library which you can try installing. For instance, if you see that it's searching for `libquadmath.0.dylib` but not finding it, you can try installing this library. In this case, this library can be installed through apt with:
+
+```bash
+sudo apt install libquadmath0
+```
+
+or through brew via:
+
+```bash
+brew install gcc
+```
+
+Alternatively, you can run your own versions of the `c2x` and `atomsk` binaries with this project. Compile them yourself however you wish - see the projects at https://github.com/codenrx/c2x and https://github.com/pierrehirel/atomsk and follow their instructions to build a binary on your system. Once you've done so, add the binary to your `$PATH`, and this project will pick that up and use it in preference to the prepackaged binary.
+
+On the other hand, it's possible that an error of this sort will occur if you have a non-working binary of one of these converters in your `$PATH`. If this might be the case, you can try removing it and see if the prepackaged binary works for you, or else recompile it to try to fix errors.
+
+## Licensing
 
 This project is provided under the Apache License version 2.0, the terms of which can be found in the file `LICENSE`.
 
-This project redistributes compiled binaries for the Atomsk and c2x converters. These are both licenced under the
+This project redistributes compiled binaries for the Atomsk and c2x converters. These are both licensed under the
 GNU General Public License version 3 and are redistributed per its terms. Any further redistribution of these binaries,
-including redistribution of this project as a whole, including them, must also follow the terms of this licence.
+including redistribution of this project as a whole, including them, must also follow the terms of this license.
 
-This requires conspicuously displaying notice of this licence, providing the text of of the licence (provided here in
+This requires conspicuously displaying notice of this license, providing the text of of the license (provided here in
 the files `psdi_data_conversion/bin/LICENSE_C2X` and `psdi_data_conversion/bin/LICENSE_ATOMSK`), and appropriately
 conveying the source code for each of these. Their respective source code may be found at:
 

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/psdi_data_conversion/app.py

@@ -5,6 +5,7 @@ Version 1.0, 8th November 2024
 This script acts as a server for the PSDI Data Conversion Service website.
 """
 
+from argparse import ArgumentParser
 import hashlib
 import os
 import json
@@ -14,6 +15,7 @@ import sys
 import traceback
 from flask import Flask, request, render_template, abort, Response
 
+import psdi_data_conversion
 from psdi_data_conversion import log_utility
 from psdi_data_conversion import constants as const
 from psdi_data_conversion.converter import run_converter
@@ -63,6 +65,20 @@ else:
         print(f"ERROR: {str(e)}")
         exit(1)
 
+# Get the maximum allowed size from the envvar for it
+ev_max_file_size = os.environ.get(const.MAX_FILESIZE_EV)
+if ev_max_file_size is not None:
+    max_file_size = float(ev_max_file_size)*const.MEGABYTE
+else:
+    max_file_size = const.DEFAULT_MAX_FILE_SIZE
+
+# And same for the Open Babel maximum file size
+ev_max_file_size_ob = os.environ.get(const.MAX_FILESIZE_OB_EV)
+if ev_max_file_size_ob is not None:
+    max_file_size_ob = float(ev_max_file_size_ob)*const.MEGABYTE
+else:
+    max_file_size_ob = const.DEFAULT_MAX_FILE_SIZE_OB
+
 app = Flask(__name__)
 
 
@@ -95,19 +111,6 @@ def get_last_sha() -> str:
 def website():
     """Return the web page along with the token
     """
-    # Get the maximum allowed size from the envvar for it
-    ev_max_file_size = os.environ.get(const.MAX_FILESIZE_EV)
-    if ev_max_file_size is not None:
-        max_file_size = float(ev_max_file_size)*const.MEGABYTE
-    else:
-        max_file_size = const.DEFAULT_MAX_FILE_SIZE
-
-    # And same for the Open Babel maximum file size
-    ev_max_file_size_ob = os.environ.get(const.MAX_FILESIZE_OB_EV)
-    if ev_max_file_size_ob is not None:
-        max_file_size_ob = float(ev_max_file_size_ob)*const.MEGABYTE
-    else:
-        max_file_size_ob = const.DEFAULT_MAX_FILE_SIZE_OB
 
     data = [{'token': token,
              'max_file_size': max_file_size,
@@ -143,7 +146,7 @@ def convert():
                                               data=request.form,
                                               to_format=request.form['to'],
                                               from_format=request.form['from'],
-                                              strict=request.form['check_ext'],
+                                              strict=(request.form['check_ext'] != "false"),
                                               log_mode=log_mode,
                                               log_level=log_level,
                                               delete_input=True,
@@ -260,3 +263,80 @@ def data():
     else:
         # return http status code 405
         abort(405)
+
+
+def start_app():
+    """Start the Flask app - this requires being run from the base directory of the project, so this changes the
+    current directory to there. Anything else which changes it while the app is running may interfere with its proper
+    execution.
+    """
+
+    os.chdir(os.path.join(psdi_data_conversion.__path__[0], ".."))
+    app.run()
+
+
+def main():
+    """Standard entry-point function for this script.
+    """
+
+    parser = ArgumentParser()
+
+    parser.add_argument("--use-env-vars", action="store_true",
+                        help="If set, all other arguments and defaults for this script are ignored, and environmental "
+                        "variables and their defaults will instead control execution. These defaults will result in "
+                        "the app running in production server mode.")
+
+    parser.add_argument("--max-file-size", type=float, default=const.DEFAULT_MAX_FILE_SIZE,
+                        help="The maximum allowed filesize in MB - 0 (default) indicates no maximum")
+
+    parser.add_argument("--max-file-size-ob", type=float, default=const.DEFAULT_MAX_FILE_SIZE_OB,
+                        help="The maximum allowed filesize in MB for the Open Babel converter, taking precendence over "
+                        "the general maximum file size when Open Babel is used - 0 indicates no maximum. Default 1 MB.")
+
+    parser.add_argument("--service-mode", action="store_true",
+                        help="If set, will run as if deploying a service rather than the local GUI")
+
+    parser.add_argument("--dev-mode", action="store_true",
+                        help="If set, will expose development elements")
+
+    parser.add_argument("--log-mode", type=str, default=const.LOG_FULL,
+                        help="How logs should be stored. Allowed values are: \n"
+                        "- 'full' - Multi-file logging, not recommended for the CLI, but allowed for a compatible "
+                        "interface with the public web app"
+                        "- 'simple' - Logs saved to one file"
+                        "- 'stdout' - Output logs and errors only to stdout"
+                        "- 'none' - Output only errors to stdout")
+
+    parser.add_argument("--log-level", type=str, default=None,
+                        help="The desired level to log at. Allowed values are: 'DEBUG', 'INFO', 'WARNING', 'ERROR, "
+                             "'CRITICAL'. Default: 'INFO' for logging to file, 'WARNING' for logging to stdout")
+
+    # Set global variables for settings based on parsed arguments, unless it's set to use env vars
+    args = parser.parse_args()
+
+    if not args.use_env_vars:
+
+        global max_file_size
+        max_file_size = args.max_file_size*const.MEGABYTE
+
+        global max_file_size_ob
+        max_file_size_ob = args.max_file_size_ob*const.MEGABYTE
+
+        global service_mode
+        service_mode = args.service_mode
+
+        global production_mode
+        production_mode = not args.dev_mode
+
+        global log_mode
+        log_mode = args.log_mode
+
+        global log_level
+        log_level = args.log_level
+
+    start_app()
+
+
+if __name__ == "__main__":
+
+    main()

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/psdi_data_conversion/converters/base.py

@@ -284,9 +284,9 @@ class FileConverter:
             if max_file_size is None:
                 from psdi_data_conversion.converters.openbabel import CONVERTER_OB
                 if self.name == CONVERTER_OB:
-                    self.max_file_size = const.DEFAULT_MAX_FILE_SIZE_OB*const.MEGABYTE
+                    self.max_file_size = const.DEFAULT_MAX_FILE_SIZE_OB
                 else:
-                    self.max_file_size = const.DEFAULT_MAX_FILE_SIZE*const.MEGABYTE
+                    self.max_file_size = const.DEFAULT_MAX_FILE_SIZE
             else:
                 self.max_file_size = max_file_size*const.MEGABYTE
 

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/psdi_data_conversion/static/content/download.htm

@@ -43,6 +43,8 @@
         Python library.
       </p>
 
+      <h2>Installation</h2>
+
       <h3>Install via pip</h3>
 
       <ul>
@@ -63,12 +65,6 @@
         Python library.
       </p>
 
-      <p>
-        If you do wish to run the local version of this webpage, you'll need to create a helper script to set up the
-        proper parameters and start the server. See the README provided on the front page of this project's PyPI page,
-        linked above, for the source of this helper script, which you can paste and use locally.
-      </p>
-
       <h3>Source Code</h3>
 
       <ul>
@@ -86,11 +82,28 @@
         for other possible optional dependencies sets that can be installed.
       </p>
 
-      <p>When installed in this manner, the helper script to run the local webpage is provided in the root directory
-        of the repository as <code class="secondary">run_local.sh</code>. It can be run from this directory, copied to
-        your <code class="secondary">$PATH</code>, or aliased as desired.
+      <h2>Use</h2>
+
+      <p>
+        Once installed, the project can be used in one of three ways:
       </p>
 
+      <ul>
+        <li><strong>Local Gui:</strong> Run the script <code class="secondary">psdi-data-convert-gui</code> to start the
+          server. Append the <code class="secondary">--help</code> option for to see optional arguments (generally not
+          required for end-users)
+        </li>
+        <li><strong>Command-Line Application:</strong> Run the script <code class="secondary">psdi-data-convert</code>
+          to use the application at the command-line. Append the <code class="secondary">--help</code> option to see
+          arguments for it, and/or find documentation in the project's README.
+        </li>
+        <li><strong>Python Library:</strong> Within a Python script, library, or terminal, the project can be imported
+          via <code class="secondary">import psdi_data_conversion</code>, with the most useful function being <code
+            class="secondary">psdi_data_conversion.converter.run_converter</code> - see the <code
+            class="secondary">help()</code> of this function and/or find documentation in the project's README.
+        </li>
+      </ul>
+
       <h2>Documentation</h2>
 
       <ul>

{psdi_data_conversion-0.0.36 → psdi_data_conversion-0.0.37}/psdi_data_conversion/static/styles/psdi-common.css

@@ -228,7 +228,7 @@ body {
   top       : 0;
   left      : 0;
   background: var(--ifm-background-color);
-  z-index   : 9999;
+  z-index   : 99999;
 }
 
 select,
@@ -412,7 +412,8 @@ h6 {
 }
 
 p {
-  margin: 0 0 1.25rem 0;
+  margin        : 0 0 1.25rem 0;
+  padding-bottom: 0;
 }
 
 .text--center {
@@ -546,9 +547,9 @@ a svg {
 }
 
 .navbar__title h5 {
-  display: unset;
+  display: flex;
   color  : var(--ifm-heading-color);
-  margin : 0 0 0.5rem 0.5rem;
+  margin : 0 0 0.5rem 1.5rem;
 }
 
 .navbar__logo img {