Move environment.yml into the root directory

Author: JohT

.github/workflows/public-analyze-code-graph.yml

@@ -109,7 +109,7 @@ jobs:
           python-version: ${{ matrix.python }}
           miniforge-version: ${{ matrix.miniforge }}
           activate-environment: codegraph
-          environment-file: ./jupyter/environment.yml
+          environment-file: ./environment.yml
           auto-activate-base: false
           show-channel-urls: true
       - name: (Python Setup) Conda environment info

COMMANDS.md

@@ -389,10 +389,10 @@ Here is an example on how to use [executeJupyterNotebook.sh](./scripts/executeJu
   conda activate codegraph
   ```
 
-  or by using the environment file [codegraph-environment.yml](./jupyter/environment.yml):
+  or by using the codegraph environment file [environment.yml](./environment.yml):
 
   ```shell
-  conda env create --file ./jupyter/environment.yml
+  conda env create --file ./environment.yml
   conda activate codegraph
   ```
 

README.md

@@ -137,7 +137,7 @@ The [Code Structure Analysis Pipeline](./.github/workflows/internal-java-code-an
 - Start [Neo4j](https://neo4j.com) Graph Database ([analysis.sh](./scripts/analysis/analyze.sh))
 - Generate CSV Reports [scripts/reports](./scripts/reports) using the command line JSON parser [jq](https://jqlang.github.io/jq)
 - Uses [Neo4j Graph Data Science](https://neo4j.com/product/graph-data-science) for community detection, centrality, similarity, node embeddings and topological sort ([analysis.sh](./scripts/analysis/analyze.sh))
-- Generate [Jupyter Notebook](https://jupyter.org) reports using these libraries specified in the [environment.yml](./jupyter/environment.yml):
+- Generate [Jupyter Notebook](https://jupyter.org) reports using these libraries specified in the [environment.yml](./environment.yml):
   - [Python](https://www.python.org)
   - [jupyter](https://jupyter.org)
   - [matplotlib](https://matplotlib.org)

jupyter/environment.yml renamed to environment.yml

@@ -3,7 +3,7 @@
 # Activates the Conda (Python package manager) environment "codegraph" with all packages needed to execute the Jupyter Notebooks.
 
 # Note: This script uses the conda environment defined in CODEGRAPH_CONDA_ENVIRONMENT (defaults to "codegraph").
-#       If the environment hadn't been created yet it will use "environment.yml" 
+#       If the environment hadn't been created yet, it will use "environment.yml" from the root directory
 #       in the same directory as the given jupyter notebook ipynb file
 #       to create the environment.
 
@@ -25,7 +25,7 @@ echo "activateCondaEnvironment: JUPYTER_NOTEBOOK_DIRECTORY=${JUPYTER_NOTEBOOK_DI
 
 # Get the file name of the environment description file for the conda package and environment manager 
 # that contains all dependencies and their versions.
-CONDA_ENVIRONMENT_FILE=${CONDA_ENVIRONMENT_FILE:-"${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml"} # Conda (package manager for Python) environment file path
+CONDA_ENVIRONMENT_FILE=${CONDA_ENVIRONMENT_FILE:-"${JUPYTER_NOTEBOOK_DIRECTORY}/../environment.yml"} # Conda (package manager for Python) environment file path
 if [ ! -f "${CONDA_ENVIRONMENT_FILE}" ] ; then
     echo "activateCondaEnvironment: Couldn't find environment file ${CONDA_ENVIRONMENT_FILE}."
     exit 2