Minor updates advances #2

.github/workflows/test_workflow.yaml

@@ -19,7 +19,7 @@ jobs:
       with:
         auto-update-conda: true
         environment-file: environment.yaml
-        activate-environment: tda-nn-separability
+        activate-environment: tda-nn-analysis
         python-version: 3.10.14
         channels: conda-forge
 

.gitignore

@@ -167,6 +167,7 @@ data/
 *.xlsx
 
 # Outputs
+outputs/*
 outputs/checkpoints/*.pth
 outputs/figures/*.png
 logs/

Makefile

@@ -1,7 +1,7 @@
-# Enhanced Makefile for managing the Conda environment tda-nn-separability
+# Makefile for managing the Conda environment tda-nn-analysis
 
 # Parameters
-ENV_NAME := tda-nn-separability
+ENV_NAME := tda-nn-analysis
 PYTHON_VERSION := 3.10
 ENV_FILE := environment.yaml
 
@@ -18,15 +18,14 @@ init:
 ifndef CONDA
 	$(error "conda is not available, please install Miniconda or Anaconda.")
 endif
-	@echo "Creating the Conda environment if it doesn't exist..."
-	@conda env list | grep -q '^$(ENV_NAME) ' || \
-	conda create --yes --name $(ENV_NAME) python=$(PYTHON_VERSION)
+	echo "Creating the Conda environment if it doesn't exist..."
+	conda env list | grep -q '^$(ENV_NAME) ' || conda create --yes --name $(ENV_NAME) python=$(PYTHON_VERSION)
 
 # Install packages from an environment file or manually specified
 .PHONY: install
 install: init
-	@echo "Installing necessary packages into the Conda environment..."
-	@if [ -f "$(ENV_FILE)" ]; then \
+	echo "Installing necessary packages into the Conda environment..."
+	if [ -f "$(ENV_FILE)" ]; then \
 		echo "Using $(ENV_FILE) to install packages..."; \
 		conda env update --name $(ENV_NAME) --file $(ENV_FILE) --prune; \
 	else \
@@ -37,25 +36,24 @@ install: init
 # Export the current environment to a YAML file, excluding build-specific fields
 .PHONY: export
 export:
-	@echo "Exporting the Conda environment to $(ENV_FILE)..."
-	@conda env export --name $(ENV_NAME) --no-builds | grep -v "^name: " > $(ENV_FILE)
+	echo "Exporting the Conda environment to $(ENV_FILE)..."
+	conda env export --name $(ENV_NAME) --no-builds | grep -v "^name: " > $(ENV_FILE)
 
 # Update all packages in the Conda environment
 .PHONY: update
 update: init
-	@echo "Updating all packages in the Conda environment..."
-	@conda run --name $(ENV_NAME) conda update --all --yes
+	echo "Updating all packages in the Conda environment..."
+	conda run --name $(ENV_NAME) conda update --all --yes
 
 # Run tests using pytest within the Conda environment
 .PHONY: test
 test: init
-	@echo "Running tests..."
+	echo "Running tests..."
 	pytest tests -v
 
 # Clean up __pycache__ directories and *.pyc files
 .PHONY: clean
 clean:
-	@echo "Cleaning up __pycache__ directories and *.pyc files..."
-	@find . -type d -name "__pycache__" -exec rm -rf {} + > /dev/null 2>&1
-	@find . -type f -name "*.pyc" -delete > /dev/null 2>&1
-
+	echo "Cleaning up __pycache__ directories and *.pyc files..."
+	find . -type d -name "__pycache__" -exec rm -rf {} + > /dev/null 2>&1
+	find . -type f -name "*.pyc" -delete > /dev/null 2>&1