Merge branch 'main' of https://github.com/hcmlab/discover

hcmlab · Oct 15, 2024 · 1dfeba0 · 1dfeba0
2 parents 8f10abe + 0a6006c
commit 1dfeba0
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diff --git a/.github/workflows/build-doc.yml b/.github/workflows/build-doc.yml
@@ -13,11 +13,17 @@ jobs:
         with:
             repository: hcmlab/discover-utils
             path: discover-utils
-            ref: refs/heads/main    
+            ref: refs/heads/main
+      - name: Checkout discover modules
+        uses: actions/checkout@master
+        with:
+          repository: hcmlab/discover-modules
+          path: docs/discover-modules
+          ref: refs/heads/main
       - uses: actions/setup-python@v3
       - name: Install dependencies
         run: |
-          pip install sphinx sphinx_rtd_theme myst-parser sphinx-argparse==0.5.2
+          pip install sphinx sphinx_rtd_theme myst-parser sphinx-argparse==0.5.2 sphinx-mdinclude
       - name: Sphinx build
         run: |
           sphinx-apidoc -e -M -d 8 -o docs/docsource/api  discover

diff --git a/README.md b/README.md
@@ -78,7 +78,7 @@ DISCOVER takes the following optional arguments as input:
 
 Internally DISCOVER converts the input to environment variables with the following names: 
 
-```DISCOVER_SERVER_HOST```, ```DISCOVER_PORT```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_CML_DIR```
+```DISCOVER_SERVER_HOST```, ```DISCOVER_PORT```, ```DISCOVER_CML_DIR```, ```DISCOVER_DATA_DIR```, ```DISCOVER_TMP_DIR```, ```DISCOVER_CML_DIR```, ```DISCOVER_LOG_DIR```
 
 
 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.

diff --git a/discover/backend/virtual_environment.py b/discover/backend/virtual_environment.py
@@ -314,7 +314,7 @@ def run_shell_script(
             raise subprocess.CalledProcessError(returncode=return_code, cmd=run_cmd)
 
     def kill(self):
-        """Kills parent and children processess"""
+        """Kills parent and children processes"""
         parent = psutil.Process(self.current_process.pid)
         # kill all the child processes
         for child in parent.children(recursive=True):

diff --git a/docs/docsource/api/.gitkeep b/docs/docsource/api/.gitkeep
diff --git a/docs/docsource/api/modules.rst b/docs/docsource/api/modules.rst
diff --git a/docs/docsource/api/nova_server.app.rst b/docs/docsource/api/nova_server.app.rst
diff --git a/docs/docsource/api/nova_server.backend.rst b/docs/docsource/api/nova_server.backend.rst
diff --git a/docs/docsource/api/nova_server.backend.virtual_environment.rst b/docs/docsource/api/nova_server.backend.virtual_environment.rst
diff --git a/docs/docsource/api/nova_server.data.adjectives.rst b/docs/docsource/api/nova_server.data.adjectives.rst
diff --git a/docs/docsource/api/nova_server.data.animals.rst b/docs/docsource/api/nova_server.data.animals.rst
diff --git a/docs/docsource/api/nova_server.data.colors.rst b/docs/docsource/api/nova_server.data.colors.rst
diff --git a/docs/docsource/api/nova_server.data.countries.rst b/docs/docsource/api/nova_server.data.countries.rst
diff --git a/docs/docsource/api/nova_server.data.languages.rst b/docs/docsource/api/nova_server.data.languages.rst
diff --git a/docs/docsource/api/nova_server.data.names.rst b/docs/docsource/api/nova_server.data.names.rst
diff --git a/docs/docsource/api/nova_server.data.rst b/docs/docsource/api/nova_server.data.rst
diff --git a/docs/docsource/api/nova_server.data.star_wars.rst b/docs/docsource/api/nova_server.data.star_wars.rst
diff --git a/docs/docsource/api/nova_server.exec.execution_handler.rst b/docs/docsource/api/nova_server.exec.execution_handler.rst
diff --git a/docs/docsource/api/nova_server.exec.rst b/docs/docsource/api/nova_server.exec.rst
diff --git a/docs/docsource/api/nova_server.route.cancel.rst b/docs/docsource/api/nova_server.route.cancel.rst
diff --git a/docs/docsource/api/nova_server.route.cml_info.rst b/docs/docsource/api/nova_server.route.cml_info.rst
diff --git a/docs/docsource/api/nova_server.route.deprecated_extract.rst b/docs/docsource/api/nova_server.route.deprecated_extract.rst
diff --git a/docs/docsource/api/nova_server.route.deprecated_train.rst b/docs/docsource/api/nova_server.route.deprecated_train.rst
diff --git a/docs/docsource/api/nova_server.route.explain.rst b/docs/docsource/api/nova_server.route.explain.rst
diff --git a/docs/docsource/api/nova_server.route.extract.rst b/docs/docsource/api/nova_server.route.extract.rst
diff --git a/docs/docsource/api/nova_server.route.fetch_result.rst b/docs/docsource/api/nova_server.route.fetch_result.rst
diff --git a/docs/docsource/api/nova_server.route.log.rst b/docs/docsource/api/nova_server.route.log.rst
diff --git a/docs/docsource/api/nova_server.route.predict.rst b/docs/docsource/api/nova_server.route.predict.rst
diff --git a/docs/docsource/api/nova_server.route.process.rst b/docs/docsource/api/nova_server.route.process.rst
diff --git a/docs/docsource/api/nova_server.route.rst b/docs/docsource/api/nova_server.route.rst
diff --git a/docs/docsource/api/nova_server.route.status.rst b/docs/docsource/api/nova_server.route.status.rst
diff --git a/docs/docsource/api/nova_server.route.train.rst b/docs/docsource/api/nova_server.route.train.rst
diff --git a/docs/docsource/api/nova_server.route.ui.rst b/docs/docsource/api/nova_server.route.ui.rst
diff --git a/docs/docsource/api/nova_server.rst b/docs/docsource/api/nova_server.rst
diff --git a/docs/docsource/api/nova_server.templates.rst b/docs/docsource/api/nova_server.templates.rst
diff --git a/docs/docsource/api/nova_server.utils.deprecated_dataset_utils.rst b/docs/docsource/api/nova_server.utils.deprecated_dataset_utils.rst
diff --git a/docs/docsource/api/nova_server.utils.deprecated_db_utils.rst b/docs/docsource/api/nova_server.utils.deprecated_db_utils.rst
diff --git a/docs/docsource/api/nova_server.utils.deprecated_explain_utils.rst b/docs/docsource/api/nova_server.utils.deprecated_explain_utils.rst
diff --git a/docs/docsource/api/nova_server.utils.env.rst b/docs/docsource/api/nova_server.utils.env.rst
diff --git a/docs/docsource/api/nova_server.utils.import_utils.rst b/docs/docsource/api/nova_server.utils.import_utils.rst
diff --git a/docs/docsource/api/nova_server.utils.job_utils.rst b/docs/docsource/api/nova_server.utils.job_utils.rst