Merge pull request #178 from birgorg/clone-br-feature

Use birgorg/bioconda-recipes

.travis.yml

@@ -49,13 +49,9 @@ install:
 
 before_script:
 
-  # Download Bioconda-recipe repository
-
-  - git clone https://github.com/bioconda/bioconda-recipes
-
   # Install bioconda-recipe-gen
 
-  - python setup.py install
+  - pip install .
 
 script:
   - travis_wait 60 ./travis/test.sh $PACKAGE

setup.py

@@ -10,7 +10,7 @@
     packages=find_packages("src"),
     package_dir={"": "src"},
     test_suite="test",
-    install_requires=['docker>=2.0.0', 'gitdb2==2.0.5', 'validators'],
+    install_requires=['docker>=2.0.0', 'gitdb2==2.0.5', 'validators', 'gitpython'],
     entry_points={
          'console_scripts': ['bioconda-recipe-gen = bioconda_recipe_gen.cli:start'],
     },

src/bioconda_recipe_gen/bioconda_recipe_gen.py

@@ -5,7 +5,6 @@
 
 from . import build
 
-
 def main(bioconda_recipe_path, recipes, build_scripts, debug):
     success = False
     while not success and build_scripts:
@@ -34,6 +33,7 @@ def main(bioconda_recipe_path, recipes, build_scripts, debug):
 
         # Sanity check
         success = build.mini_sanity_check(bioconda_recipe_path, recipe)
+
         # copy the final recipe into the current directory
         copyfile(
             os.path.join(recipe.path, "meta.yaml"),

src/bioconda_recipe_gen/cli.py

@@ -3,32 +3,24 @@
 import sys
 import logging
 from shutil import rmtree
+from tempfile import TemporaryDirectory
+from git import Repo
 
 from .bioconda_recipe_gen import main
 from .preprocessors.from_files import preprocess as files_preprocess
 from .preprocessors.sdist_optimization import sdist_optimization
 from .template_generation import init
 
-def bioconda_recipes_exists(path):
-    recipes_path = os.path.join(path, "recipes")
-    config_path = os.path.join(path, "config.yml")
-    return os.path.exists(recipes_path) and os.path.exists(config_path)
-
-
-def call_main(args, recipes, build_scripts):
-    if bioconda_recipes_exists(args.bioconda_recipe_path):
-        main(args.bioconda_recipe_path, recipes, build_scripts, args.debug)
-    else:
-        sys.exit("ERROR: Wrong path to bioconda-recipes")
-
+BIOCONDA_RECIPES = 'https://github.com/birgorg/bioconda-recipes'
 
 def build(args):
-    recipes, build_scripts = files_preprocess(args)
-    if args.strategy == "python3" or args.strategy == "python2":
-        for recipe in recipes:
-            sdist_optimization(recipe)
-    call_main(args, recipes, build_scripts)
-
+    with TemporaryDirectory() as bioconda_recipe_path:
+        _ = Repo.clone_from(BIOCONDA_RECIPES, bioconda_recipe_path)
+        recipes, build_scripts = files_preprocess(args, bioconda_recipe_path)
+        if args.strategy == "python3" or args.strategy == "python2":
+            for recipe in recipes:
+                sdist_optimization(recipe)
+        main(bioconda_recipe_path, recipes, build_scripts, args.debug)
 
 def setup_logging(debug, output_dir_path):
     if debug:
@@ -69,10 +61,6 @@ def start():
         "build",
         help="Build the recipe from the template generate by 'init'"
     )
-    parser_files.add_argument(
-        "bioconda_recipe_path",
-        help="Path to your local copy of the bioconda-recipe repository",
-    )
     parser_files.add_argument(
         "recipe_path",
         help="Path to folder with meta.yaml and build.sh templates",

src/bioconda_recipe_gen/preprocessors/from_files.py

@@ -136,8 +136,8 @@ def create_build_script(recipe, args, filesystem):
     return build_script
 
 
-def preprocess(args):
-    recipe = create_recipe(args.bioconda_recipe_path, args.recipe_path, args.strategy)
+def preprocess(args, bioconda_recipe_path):
+    recipe = create_recipe(bioconda_recipe_path, args.recipe_path, args.strategy)
     with tempfile.TemporaryDirectory() as tmpdir:
         download_and_unpack_source(recipe.url, tmpdir)
         source_path = os.path.join(tmpdir, "source")

src/bioconda_recipe_gen/template_generation.py

@@ -79,7 +79,7 @@ def create_path(name):
     return path
 
 
-def init(args):
+def init(_):
     name, version, url, strategy = get_user_input()
     path = create_path(name)
     recipe = make_recipe(name, version, url, path, strategy)

travis/test.sh

@@ -1,45 +1,44 @@
 #!/bin/bash
 ##### Constants
 # The TRAVIS_BUILD_DIR is specified by travis itself
-BR_PATH=$TRAVIS_BUILD_DIR/bioconda-recipes
 DATA_PATH=$TRAVIS_BUILD_DIR/travis/data
 
 ##### functions
 
 build_htstream()
 {
     data=$DATA_PATH/htstream
-    bioconda-recipe-gen build $BR_PATH $data cmake
+    bioconda-recipe-gen build $data cmake
 }
 
 build_qfilt()
 {
     data=$DATA_PATH/qfilt
-    bioconda-recipe-gen build $BR_PATH $data cmake
+    bioconda-recipe-gen build $data cmake
 }
 
 build_libdivsufsort()
 {
     data=$DATA_PATH/libdivsufsort
-    bioconda-recipe-gen build $BR_PATH $data cmake
+    bioconda-recipe-gen build $data cmake
 }
 
 build_lambda()
 {
     data=$DATA_PATH/lambda
-    bioconda-recipe-gen build $BR_PATH $data cmake
+    bioconda-recipe-gen build $data cmake
 }
 
 build_fuma()
 {
     data=$DATA_PATH/fuma
-    yes | bioconda-recipe-gen build $BR_PATH $data python2
+    yes | bioconda-recipe-gen build $data python2
 }
 
 build_crossmap()
 {
     data=$DATA_PATH/crossmap
-    yes | bioconda-recipe-gen build $BR_PATH $data python3
+    yes | bioconda-recipe-gen build $data python3
 }