Adding comments + doc. Starting the work on git packages.

ecg.py

@@ -1,5 +1,13 @@
 #!/bin/python3
 
+"""
+    ECG is program that automates software environment checking
+    in scientific artifacts.
+
+    It is meant to be executed periodically to analyze variations in the
+    software environment of the artifact through time.
+"""
+
 import subprocess
 import json
 import yaml
@@ -10,20 +18,42 @@ import requests
 import zipfile
 import io
 import tarfile
-
 import pathlib
-HEREPATH = pathlib.Path(__file__).parent.absolute()
+import logging
 
+# Paths:
+HEREPATH = pathlib.Path(__file__).parent.absolute()
 # Where to store list of installed packages:
 PKGLISTS = "./pkglists/"
 
-# Commands to list installed packages along with their versions and the name of the package manager, depending on the packages manager:
+# Commands to list installed packages along with their versions and the name
-pkgmgr_cmd = {"dpkg":"dpkg -l | awk 'NR>5 {print $2 \",\" $3 \",\" \"dpkg\"}'", "rpm":"rpm -qa --queryformat '%{NAME},%{VERSION},rpm\\n'", "pacman":"pacman -Q | awk '{print $0 \",\" $1 \",pacman\"}'", "pip":"pip freeze | sed 's/==/,/g' | awk '{print $0 \",pip\"}'", "conda":"/root/.conda/bin/conda list -e | sed 's/=/ /g' | awk 'NR>3 {print $1 \",\" $2 \",conda\"}'"}
+# of the package manager, depending on the package managers:
+pkgmgr_cmd = {
+    "dpkg":"dpkg -l | awk 'NR>5 {print $2 \",\" $3 \",\" \"dpkg\"}'", \
+    "rpm":"rpm -qa --queryformat '%{NAME},%{VERSION},rpm\\n'", \
+    "pacman":"pacman -Q | awk '{print $0 \",\" $1 \",pacman\"}'", \
+    "pip":"pip freeze | sed 's/==/,/g' | awk '{print $0 \",pip\"}'", \
+    "conda":"/root/.conda/bin/conda list -e | sed 's/=/ /g' | awk 'NR>3 {print $1 \",\" $2 \",conda\"}'", \
+    "git":""
+}
 
-import logging
+# Enables logging:
 logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO)
 
 def download_sources(config):
+    """
+        Downloads the source of the artifact in 'config'.
+
+        Parameters
+        ----------
+        config: dict
+            Parsed YAML config file.
+
+        Returns
+        -------
+        tempdir: tempfile.TemporaryDirectory
+            The directory where the artifact is downloaded to.
+    """
     url = config["artifact_url"]
     logging.info(f"Downloading sources from {url}")
     temp_dir = tempfile.TemporaryDirectory()
@@ -37,6 +67,23 @@ def download_sources(config):
     return temp_dir
 
 def build_image(config, src_dir):
+    """
+        Builds the given Docker image in 'config'.
+
+        Parameters
+        ----------
+        config: dict
+            Part of the parsed YAML config file concerning the Docker image
+            to build.
+
+        src_dir: tempfile.TemporaryDirectory
+            The directory where the artifact is stored.
+
+        Returns
+        -------
+        return_code: int
+            Return code of the Docker 'build' command.
+    """
     name = config["name"]
     logging.info(f"Starting building image {name}")
     path = os.path.join(src_dir, config["location"])
@@ -49,6 +96,24 @@ def build_image(config, src_dir):
     return return_code == 0
 
 def check_env(config, src_dir):
+    """
+        Builds a list of all software packages installed in the
+        Docker image given in 'config', depending on the package managers
+        specified in the configuration, then stores it in a CSV file.
+
+        Parameters
+        ----------
+        config: dict
+            Part of the parsed YAML config file concerning the Docker image
+            where to check the environment.
+
+        src_dir: tempfile.TemporaryDirectory
+            The directory where the artifact is stored.
+
+        Returns
+        -------
+        None
+    """
     pathlib.Path(PKGLISTS).mkdir(parents=True, exist_ok=True)
     path = os.path.join(src_dir, config["location"])
     pkglist_file = open(PKGLISTS + "pkglist.csv", "w")
@@ -59,14 +124,45 @@ def check_env(config, src_dir):
         pkglist = check_process.stdout.decode("utf-8")
         print(pkglist)
         pkglist_file.write(pkglist)
+    if "git_packages" in config.keys():
+        print(config["git_packages"])
     pkglist_file.close()
 
 def remove_image(config):
+    """
+        Removes the Docker image given in 'config'.
+
+        Parameters
+        ----------
+        config: dict
+            Part of the parsed YAML config file concerning the Docker image
+            to remove.
+
+        Returns
+        -------
+        None
+    """
     name = config["name"]
     logging.info(f"Removing image '{name}'")
     subprocess.run(["docker", "rmi", name])
 
 def build_images(config, src_dir):
+    """
+        Builds all Docker images specified in 'config', checks software
+        environment if build is successful, then removes the images.
+
+        Parameters
+        ----------
+        config: dict
+            Parsed YAML config file.
+
+        src_dir: tempfile.TemporaryDirectory
+            The directory where the artifact is stored.
+
+        Returns
+        -------
+        None
+    """
     for image in config["dockerfiles"]:
         successful_build = build_image(image, src_dir)
         if successful_build:
@@ -74,13 +170,15 @@ def build_images(config, src_dir):
             remove_image(image)
 
 def main():
+    # Command line arguments parser:
     parser = argparse.ArgumentParser(
                     prog='ecg',
                     description='Check if a dockerfile is still buildable')
     parser.add_argument('config')
     parser.add_argument('-v', '--verbose', action='store_true')
-
     args = parser.parse_args()
+
+    # Parsing the input YAML file including the configuration of the artifact:
     config = None
     with open(args.config, "r") as config_file:
         config = yaml.safe_load(config_file)

example.yaml

@@ -5,7 +5,10 @@ dockerfiles:
   - name: "image1:version"
     location: "path/to/docker/folder"
     package_managers:
-      - "dpkg" # Possible values: dpkg, pip, conda
+      - "dpkg" # Possible values: dpkg, rpm, pacman, pip, conda
+    git_packages:
+      - name: "pkg1"
+        location: "path/to/git/package"
   - name: "image2:version"
     location: "path/to/docker/folder"
     package_managers:

test.yaml

@@ -7,3 +7,6 @@ dockerfiles:
     package_managers:
       - "dpkg"
       - "pip"
+    git_packages:
+      - name: "pkg1"
+        location: "./pkg1"