Dev

.github/workflows/build_dist.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: "3.9"
+        python-version: "3.10"
 
     - name: Install dependencies
       run: |

.github/workflows/docs.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: "3.9"
+        python-version: "3.10"
 
     - name: Install dependencies
       run: |

.github/workflows/tests.yml

@@ -19,10 +19,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: "3.9"
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -38,18 +38,17 @@ jobs:
     - name: Test with pytest
       run: |
         python run_pytests.py tests --N_RANDOM_TESTS_PER_CASE=10 --run_slow=False
-        coverage-lcov
 
   Run-tests-on-Windows:
     name: Run tests on Windows-latest
     runs-on: windows-latest
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: "3.9"
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

Dockerfile

@@ -0,0 +1,45 @@
+FROM python:3.10-slim AS base_stage
+ENV ROOT_DIR=/PythonProject-Template
+ARG MODE=release
+# MODE: 'release' or 'it' (will be interpreted as debug). This is used in the docker_entrypoint.sh script
+ENV MODE=${MODE}
+
+# Build stage
+FROM base_stage AS build_stage
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# System dependencies
+RUN apt update -y &&  \
+    apt install -y --no-install-recommends build-essential git dos2unix &&  \
+    rm -rf /var/lib/apt/lists/*
+
+# Files
+WORKDIR "$ROOT_DIR"
+COPY *_requirements.txt requirements.txt *.toml *.lock *.py ./
+COPY src src
+COPY dist dist
+COPY docker_files docker_files
+RUN dos2unix docker_files/*.sh
+
+# Virtual environment
+RUN python3 -m venv ./venv &&  \
+    . ./venv/bin/activate &&  \
+    pip install --upgrade pip &&  \
+    pip install poetry &&  \
+    poetry install --no-interaction --no-ansi
+
+# rm unnecessary files
+RUN rm -rf *_requirements.txt requirements.txt *.toml *.lock setup.py run_pytests.py src/*.egg-info dist
+
+# Main stage
+FROM base_stage AS main_stage
+
+# Files
+WORKDIR $ROOT_DIR
+COPY --from=build_stage $ROOT_DIR ./
+VOLUME data
+
+# Entrypoint
+ENV PATH="venv/bin:$PATH"
+ENTRYPOINT ["bash", "docker_files/docker_entrypoint.sh"]

change_project_name.py

@@ -174,6 +174,19 @@ def update_docs_yml(args):
     return 0
 
 
+def update_dockerfile(args):
+    if not os.path.exists("Dockerfile"):
+        return 0
+    with open("Dockerfile", "r") as f:
+        content = f.read()
+    root_dir = os.path.basename(os.path.dirname(__file__))
+    print(f"ROOT_DIR=/{root_dir}")
+    content = re.sub(r'ENV ROOT_DIR=/(.*?)\n', f'ENV ROOT_DIR=/{root_dir}\n', content)
+    with open("Dockerfile", "w") as f:
+        f.write(content)
+    return 0
+
+
 def main():
     parser = get_parser()
     args = parser.parse_args()
@@ -198,7 +211,7 @@ def main():
     update_readme_md(args)
     update_license(args)
     update_docs_yml(args)
-
+    update_dockerfile(args)
     return 0
 
 

docker_files/build_image_and_run.py

@@ -0,0 +1,143 @@
+import os
+import argparse
+import subprocess
+import json
+import time
+from typing import Optional
+
+
+def get_args_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--dockerfiles_folder",
+        type=str,
+        default=os.path.join(os.path.dirname(__file__), ".."),
+    )
+    parser.add_argument(
+        "--tag",
+        type=str,
+        default="latest",
+    )
+    parser.add_argument(
+        "--image_name",
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        "--mode",
+        type=str,
+        default="release",
+        choices=["release", "data", "trainings", "analysis", "it"],
+        help="Mode of the project to run the container for. \n"
+             "- release: This mode is responsible for running the __main__.py of the current package. \n"
+             "- it: This is a development mode that is responsible for running the container in the interactive mode.",
+    )
+    parser.add_argument(
+        "--args",
+        type=str,
+        default=None,
+        help="Arguments to pass to the container as a JSON string "
+    )
+    parser.add_argument(
+        "--only_run",
+        action=argparse.BooleanOptionalAction,
+        default=False,
+        help="If set, only runs the container without building the image.",
+    )
+    return parser
+
+
+def build_images(
+        *,
+        dockerfiles_folder: str = ".",
+        tag: str = "latest",
+        image_name: Optional[str] = None,
+):
+    if not image_name:
+        image_name = os.path.basename(os.path.dirname(os.path.dirname(__file__)))
+    images = []
+    for root, dirs, files in os.walk(dockerfiles_folder):
+        for file in files:
+            if not file.startswith("Dockerfile"):
+                continue
+            post_name = file.replace("Dockerfile", "")
+            full_image_name = f"{image_name}{post_name}:{tag}"
+            print(f"Building image {full_image_name} from {os.path.join(root, file)}")
+            cmd = f"docker build -t {full_image_name} -f {os.path.join(root, file)} ."
+            print(f"{cmd = }")
+            subprocess.run(cmd, shell=True, check=True, cwd=root)
+            print(f"Built image {full_image_name}")
+            images.append(full_image_name)
+    print(f"Pruning old images")
+    cmd = "docker image prune --force"
+    print(f"{cmd = }")
+    subprocess.run(cmd, shell=True, check=True)
+    print(f"Pruned old images")
+    return images
+
+def run_container(
+        *,
+        container_name: str = None,
+        image_name: str = None,
+        tag: str = "latest",
+        args: list = None,
+        run_args: list = None,
+):
+    root_folder_name = os.path.basename(os.path.dirname(os.path.dirname(__file__)))
+    if not container_name:
+        container_name = f"{image_name}-container"
+    if not image_name:
+        image_name = root_folder_name
+    if ":" in image_name:
+        image_name, tag = image_name.split(":")
+    print(f"Removing container {container_name} if it exists")
+    cmd = f"docker rm --force {container_name}"
+    print(f"{cmd = }")
+    subprocess.run(cmd, shell=True, check=False)
+    print(f"Removed container {container_name}")
+    time.sleep(1)
+    print("-" * 80)
+    print(f"Running container {container_name} from image {image_name}:{tag}")
+    container_args = [
+        "--name", container_name,
+        "--detach",
+        f"--volume="
+        f"{os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'data'))}"
+        f":/{root_folder_name}/data",
+    ]
+    run_args_str = " ".join([str(arg) for arg in run_args]) if run_args else ""
+    cmd = f"docker run {' '.join(container_args)} {run_args_str} {image_name}:{tag}"
+    if args:
+        cmd += " " + " ".join([str(arg) for arg in args])
+    print(f"{cmd = }")
+    subprocess.run(cmd, shell=True, check=True)
+    print(f"Container {container_name} is now running in the background.")
+    return
+
+def main():
+    args = get_args_parser().parse_args()
+    if not args.image_name:
+        args.image_name = os.path.basename(os.path.dirname(os.path.dirname(__file__)))
+    print(f"Running with args: {json.dumps(vars(args), indent=4)}")
+    if args.only_run:
+        images = [f"{args.image_name}:{args.tag}"]
+    else:
+        images = build_images(
+            dockerfiles_folder=args.dockerfiles_folder,
+            tag=args.tag,
+            image_name=args.image_name,
+        )
+    for image in images:
+        run_container(
+            image_name=image,
+            tag=args.tag,
+            args=json.loads(args.args) if args.args else None,
+            container_name=f"{args.image_name}-{args.mode}",
+            run_args=["-e", f"MODE={args.mode}"],
+        )
+    return 0
+
+
+if __name__ == "__main__":
+    exit(main())
+

docker_files/docker_entrypoint.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+if [ -z "$ROOT_DIR" ]; then
+    echo "ROOT_DIR is not set. Exiting."
+    exit 1
+fi
+
+if [ -z "$MODE" ]; then
+    MODE="release"
+fi
+
+source venv/bin/activate
+echo "Working directory: $(pwd)"
+echo "Running in mode $MODE."
+
+if [ "$MODE" = "release" ]; then
+    python3 -m "$ROOT_DIR" "$@"
+fi
+if [ "$MODE" = "it" ]; then
+    bash
+fi
+echo "Completed in mode $MODE."

pyproject.toml

@@ -8,20 +8,21 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Operating System :: OS Independent",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
     "numpy>=1.29.5",
     "setuptools>=65.5.1",
     "pytest>=7.4.2",
     "pytest-cov>=4.1.0",
     "pytest_json_report>=1.5.0",
     "pythonbasictools>=0.0.1a11",
-    "psutil>=5.9.6"
+    "psutil>=5.9.6",
+    "docutils>=0.21.2",
 ]
 license={file="LICENSE"}