Workflow test branch

.github/workflows/build-doc.yml

@@ -17,15 +17,17 @@ jobs:
       - uses: actions/setup-python@v3
       - name: Install dependencies
         run: |
-          pip install sphinx sphinx_rtd_theme myst-parser
+          pip install sphinx sphinx_rtd_theme myst-parser sphinx-argparse==0.5.2
       - name: Sphinx build
         run: |
+          sphinx-apidoc -e -M -d 8 -o docs/docsource/api  discover
+          sphinx-apidoc -e -M -d 8 -o docs/docsource/api discover-utils/discover_utils discover-utils/discover_utils/scripts/extract.py discover-utils/discover_utils/scripts/train.py discover-utils/discover_utils/scripts/predict.py
           sphinx-build discover-utils/docs/docsource _build
           sphinx-build docs/docsource _build
 
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        if: ${{ github.event_name == 'push' }} # && github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -23,28 +23,34 @@ Use Cases
 
 DISCOVER provides a set of blueprints for exploratory data analysis, serving as a starting point for researchers to engage in detailed behavioral analysis.
 
-### Prerequesites
+### Prerequesites
 
-Before starting to install NOVA-Server you need to install Python and FFMPEG. While other Python versions may work as well the module is only tested for the following versions:
+Before starting to install DISCOVER you need to install Python and FFMPEG.
+While other Python versions may work as well the module is only tested for the following versions:
 
-3.9.x
-You can download the current version of python for your system here.
+* 3.9.x
+* 3.10.x
+* 3.11.x
 
-Download the current version off FFMPEG binaries from here for your system and make sure to extract them to a place that is in your system path. It is recommended to setup a separate virtual environment to isolate the NOVA server installation from your system python installation. To do so, open a terminal at the directory where your virtual environment should be installed and paste the following command:
+You can download the current version of python for your system [here](https://www.python.org/downloads/).
 
-python -m venv nova-server-venv
+Download the current version off FFMPEG binaries from [here](https://github.com/BtbN/FFmpeg-Builds/releases) for your system and make sure to extract them to a place that is in your system path.
+It is recommended to setup a separate virtual environment to isolate the NOVA server installation from your system python installation.
+To do so, open a terminal at the directory where your virtual environment should be installed and paste the following command:
+
+```python -m venv discover-venv```
 
 You can then activate the virtual environment like this:
 
-.\nova-server-venv\Scripts\activate
+```.\discover-venv\Scripts\activate```
 
-Setup
+### Setup
 
-Install NOVA-Server using pip like this:
+Install DISCOVER using pip like this:
 
-pip install hcai-nova-server
+```pip install hcai-discover```
 
-Start the server
+### Start the server
 
 To start DISCOVER you just open a Terminal and type
 
@@ -74,11 +80,13 @@ Internally DISCOVER converts the input to environment variables with the followi
 
 ```DISCOVER_SERVER_HOST```, ```DISCOVER_PORT```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```
 
-All variables can be either passed directly as commandline argument, set in a dotenv file or as system wide environment variables. During runtime the arguments will be prioritized in this order commandline arguments -> dotenv file -> environment variable -> default value.
 
-If the server started successfully your console output should look like this:
+All variables can be either passed directly as commandline argument, set in a [dotenv](https://hexdocs.pm/dotenvy/dotenv-file-format.html) file or as system wide environment variables.
+During runtime the arguments will be prioritized in this order commandline arguments -> dotenv file -> environment variable -> default value.
 
-Starting DISCOVER ...
+If the server started successfully your console output should look like this:
+```
+Starting DISCOVER v1.0.0...
 HOST: 0.0.0.0
 PORT: 8080
 DISCOVER_CML_DIR : cml
@@ -87,8 +95,9 @@ DISCOVER_CACHE_DIR : cache
 DISCOVER_TMP_DIR : tmp
 DISCOVER_LOG_DIR : log
 ...done
+```
 
-You can find the full documentation of the project [here](https://hcmlab.github.io/discover/docbuild/).
+You can find the full documentation of the project [here](https://hcmlab.github.io/discover).
 
 ## Citation
 If you use DISCOVER consider citing the following paper: 

discover/app.py

@@ -215,6 +215,7 @@ def resolve_arg(arg_val, env_var, arg_default_val, create_directory=False):
     os.environ[env.VENV_LOG_VERBOSE] = resolve_arg(
         "True", env.VENV_LOG_VERBOSE, "True"
     )
+
     print("...done")
     tempfile.tempdir = os.environ[env.DISCOVER_TMP_DIR]
     host = os.environ[env.DISCOVER_HOST]

discover/backend/virtual_environment.py

@@ -40,11 +40,11 @@ class VenvHandler:
     Example:
         >>> import logging
         >>> load_dotenv("../.env")
-        >>> log_dir = Path(os.getenv('NOVA_LOG_DIR', '.'))
+        >>> log_dir = Path(os.getenv('DISCOVER_LOG_DIR', '.'))
         >>> log_file = log_dir / 'test.log'
         >>> logging.basicConfig(filename=log_file, encoding='utf-8', level=logging.DEBUG)
         >>> logger = logging.getLogger('test_logger')
-        >>> module_path = Path(os.getenv("NOVA_CML_DIR")) / "test"
+        >>> module_path = Path(os.getenv("DISCOVER_CML_DIR")) / "test"
         >>> venv_handler = VenvHandler(module_path, logger=logger, log_verbose=True)
         >>> venv_handler.run_python_script_from_file(
         ...     module_path / "test.py",

discover/exec/execution_handler.py

@@ -70,7 +70,7 @@ def _nova_server_env_to_arg(self):
             env.DISCOVER_DATA_DIR,
             env.DISCOVER_LOG_DIR,
             env.DISCOVER_CACHE_DIR,
-            env.NOVA_SERVER_TMP_DIR,
+            env.DISCOVER_TMP_DIR,
             env.DISCOVER_VIDEO_BACKEND,
         ]
 
@@ -99,7 +99,7 @@ def run(self):
             # Add dotenv variables to arguments for script
             self._script_arguments |= self._nova_server_env_to_arg()
             self._script_arguments.setdefault(
-                "--shared_dir", os.getenv(env.NOVA_SERVER_TMP_DIR)
+                "--shared_dir", os.getenv(env.DISCOVER_TMP_DIR)
             )
 
             args = []
@@ -115,12 +115,12 @@ def run(self):
             # Setup virtual environment
             cml_dir = os.getenv(env.DISCOVER_CML_DIR)
             if cml_dir is None:
-                raise ValueError(f"NOVA_CML_DIR not set")
+                raise ValueError(f"DISCOVER_CML_DIR not set")
 
             module_dir = Path(cml_dir) / self.module_name
             if not module_dir.is_dir():
                 raise NotADirectoryError(
-                    f"NOVA_CML_DIR {module_dir} is not a valid directory"
+                    f"DISCOVER_CML_DIR {module_dir} is not a valid directory"
                 )
 
             extra_index_urls = os.getenv(env.VENV_EXTRA_INDEX_URLS, None)
@@ -140,7 +140,7 @@ def run(self):
             # Add dotenv variables to arguments for script
             self._script_arguments |= self._nova_server_env_to_arg()
             self._script_arguments.setdefault(
-                "--shared_dir", os.getenv(env.NOVA_SERVER_TMP_DIR)
+                "--shared_dir", os.getenv(env.DISCOVER_TMP_DIR)
             )
 
             self.backend_handler.run_shell_script(

discover/route/fetch_result.py

@@ -101,7 +101,7 @@ def fetch_thread():
         if isinstance(delete_after_download, str):
             delete_after_download = string_to_bool(delete_after_download)
 
-        shared_dir = os.getenv(env.NOVA_SERVER_TMP_DIR)
+        shared_dir = os.getenv(env.DISCOVER_TMP_DIR)
         job_dir = Path(shared_dir) / job_id
 
         if not job_dir.exists():