Merge pull request #1 from cokelaer/main

some cleanup and add singularity/seqtk cases

.github/workflows/main.yml

@@ -44,14 +44,20 @@ jobs:
         sudo apt install -y apptainer
         singularity version
 
+    - name: install tools
+      run: |
+        sudo apt install -y bwa bedtools 
+        sudo apt install -y fastqc
+
     - name: Set up Python 3.X
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
 
     - name: Install Versionix using pip
       run: |
-        pip install .[testing]
+        pip install .
+        pip install pytest pytest-cov coverage coveralls
 
     - name: Install Damona using pip
       run: |
@@ -60,18 +66,9 @@ jobs:
         damona
         echo " source ~/.config/damona/damona.sh" >> ~/.bashrc
 
-    - name: install some tools for testing
+    - name: testing
       run: |
-        damona create TEST
-        damona activate TEST
-        damona install bwa
-        damona install fastqc
-
         pytest --cov-report term --cov=versionix
-      env:
-        DAMONA_EXE: /usr/share/miniconda/bin/damona
-        DAMONA_PATH: /home/runner/.config/damona
-        DAMONA_SINGULARITY_OPTIONS: ""
 
     - name: coveralls
       run: |

test/test_parser.py

@@ -2,5 +2,13 @@
 
 
 
+
 def test_version():
-    get_version("ls")
+
+    assert get_version("ls")
+    assert get_version("singularity")
+
+
+    # stable versions can be checked 
+    assert  get_version("bwa") == "0.7.17-r1188"
+    assert  get_version("bedtools").startswith("v2")

versionix/parser.py

@@ -15,12 +15,24 @@
 import sys
 
 
-
 def parse_click():
-    """versionix, version 0.1.0"""
+    """one liner output
+
+    versionix, version 0.1.0
+
+    """
     raise NotImplementedError
 
 
+def parse_standalone_version_version(stdout: str):
+    """one liner output
+
+    singularity version 3.6.2+12-gad3457a9a
+
+    """
+    return stdout.strip().split()
+
+
 def parser_Version_column_version(stdout: str, *args):
     """
 
@@ -35,32 +47,23 @@ def parser_Version_column_version(stdout: str, *args):
 def parser_standalone_version(stdout: str, standalone, *args):
     """
 
-    STANDALONE: 1.0.0
+    STANDALONE 1.0.0
 
     """
     for line in stdout.split("\n"):
         if line.startswith(f"{standalone}"):
             return line.strip().split()[1].strip()
 
-
 metadata = {
     "default": {"caller": "--version", "parser": None, "citation": "undefined"},
     "bwa": {"caller": "stderr", "parser": parser_Version_column_version, "citation": "undefined"},
-    "bamtools": {"caller": "--version", "parser": parser_standalone_version}
-    # "art_454":{
-    #    "caller": "stdout",
-    #    "parser":  parser_name_Version_version
-    # }
+    "seqtk": {"caller": "stderr", "parser": parser_Version_column_version, "citation": "undefined"},
+    "bamtools": {"caller": "--version", "parser": parser_standalone_version},
+    "singularity": {"caller": "version", "parser": None},
+    "bedtools": {"caller": "--version", "parser": parser_standalone_version}
 }
 
 
-def base_version_parser(stdout: str):
-    """{NAME}: v1.0.0"""
-    return stdout.split("\n", 1)[0].split()[-1]
-
-
-def seqtk_version_parser(stderr: str):
-    return stderr.strip().split("\n")[1].split()[-1]
 
 
 def get_version_method_long_argument(standalone):
@@ -72,10 +75,6 @@ def get_version_method_long_argument(standalone):
         return output
 
     except subprocess.CalledProcessError as e:
-        # --version flag not available, try other flags
-        # error_message = e.stderr.strip()
-        # if error_message:
-        #    return error_message
         pass
 
 
@@ -92,7 +91,7 @@ def get_version_method_short_argument(standalone):
 
 def get_version_method_subcommand(standalone):
 
-    # Try -v flag
+    # Try subcommand
     try:
         command = [standalone, "version"]
         output = subprocess.check_output(command, stderr=subprocess.PIPE, universal_newlines=True)
@@ -116,8 +115,9 @@ def get_version(standalone, debug=False):
 
     meta = metadata.get(standalone, metadata.get("default"))
 
+
     # Case when the standalone prints information on stderr
-    # e.g. bwa
+    # e.g. bwa, seqtk
     if meta["caller"] == "stderr":
         command = [standalone]
         try:
@@ -127,9 +127,28 @@ def get_version(standalone, debug=False):
         except subprocess.CalledProcessError as e:
             print(e)
             pass
-
+    elif meta['caller'] == 'version':
+        version = get_version_method_subcommand(standalone)
+        if meta["parser"]:
+            return meta["parser"](version)
+        elif version:
+            return version
+    elif meta['caller'] == '--version':
+        version = get_version_method_long_argument(standalone)
+        if meta["parser"]:
+            return meta["parser"](version, standalone)
+        elif version:
+            return version
+    elif meta['caller'] == 'standalone':
+        version = get_version_method_subcommand(standalone)
+        if meta["parser"]:
+            return meta["parser"](version)
+        elif version:
+            return version
+
+
+    #if caller is not define fallback on --version / -v / version cases
     # bamtools hides the --version and then prints somewhere: "bamtools 1.0.0"
-    #
     version = get_version_method_long_argument(standalone)
     if meta["parser"]:
         return meta["parser"](version, standalone)

versionix/scripts.py

@@ -21,10 +21,6 @@
 ###########################################################################
 """.. rubric:: Standalone application dedicated to Damona"""
 import click
-import time
-import sys
-import pathlib
-import os
 
 
 from versionix import version
@@ -35,8 +31,8 @@
 
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
-@click.command()
 
+@click.command()
 @click.argument("standalone", required=True, type=click.STRING)
 @click.version_option(version)
 def main(**kwargs):
@@ -45,5 +41,4 @@ def main(**kwargs):
         versionix fastqc
 
     """
-
-    print(get_version(kwargs["standalone"])) # frmt=kwargs["format"]))
+    print(get_version(kwargs["standalone"]))