Migrate to conda-build 3.

.circleci/setup.sh

@@ -28,6 +28,7 @@ if [[ ! -d $WORKSPACE/miniconda ]]; then
     bash miniconda.sh -b -p $WORKSPACE/miniconda
 
     # step 2: setup channels
+
     conda config --system --add channels defaults
     conda config --system --add channels conda-forge
     conda config --system --add channels bioconda

.gitignore

@@ -7,7 +7,7 @@ test/.coverage
 .coverage
 htmlcov/
 docs/recipes/
-
+.pytest_cache
 
 # Mac OS Files
-.DS_Store
+.DS_Store

.ropeproject/config.py

@@ -0,0 +1,112 @@
+# The default ``config.py``
+# flake8: noqa
+
+
+def set_prefs(prefs):
+    """This function is called before opening the project"""
+
+    # Specify which files and folders to ignore in the project.
+    # Changes to ignored resources are not added to the history and
+    # VCSs.  Also they are not returned in `Project.get_files()`.
+    # Note that ``?`` and ``*`` match all characters but slashes.
+    # '*.pyc': matches 'test.pyc' and 'pkg/test.pyc'
+    # 'mod*.pyc': matches 'test/mod1.pyc' but not 'mod/1.pyc'
+    # '.svn': matches 'pkg/.svn' and all of its children
+    # 'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o'
+    # 'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o'
+    prefs['ignored_resources'] = ['*.pyc', '*~', '.ropeproject',
+                                  '.hg', '.svn', '_svn', '.git', '.tox']
+
+    # Specifies which files should be considered python files.  It is
+    # useful when you have scripts inside your project.  Only files
+    # ending with ``.py`` are considered to be python files by
+    # default.
+    #prefs['python_files'] = ['*.py']
+
+    # Custom source folders:  By default rope searches the project
+    # for finding source folders (folders that should be searched
+    # for finding modules).  You can add paths to that list.  Note
+    # that rope guesses project source folders correctly most of the
+    # time; use this if you have any problems.
+    # The folders should be relative to project root and use '/' for
+    # separating folders regardless of the platform rope is running on.
+    # 'src/my_source_folder' for instance.
+    #prefs.add('source_folders', 'src')
+
+    # You can extend python path for looking up modules
+    #prefs.add('python_path', '~/python/')
+
+    # Should rope save object information or not.
+    prefs['save_objectdb'] = True
+    prefs['compress_objectdb'] = False
+
+    # If `True`, rope analyzes each module when it is being saved.
+    prefs['automatic_soa'] = True
+    # The depth of calls to follow in static object analysis
+    prefs['soa_followed_calls'] = 0
+
+    # If `False` when running modules or unit tests "dynamic object
+    # analysis" is turned off.  This makes them much faster.
+    prefs['perform_doa'] = True
+
+    # Rope can check the validity of its object DB when running.
+    prefs['validate_objectdb'] = True
+
+    # How many undos to hold?
+    prefs['max_history_items'] = 32
+
+    # Shows whether to save history across sessions.
+    prefs['save_history'] = True
+    prefs['compress_history'] = False
+
+    # Set the number spaces used for indenting.  According to
+    # :PEP:`8`, it is best to use 4 spaces.  Since most of rope's
+    # unit-tests use 4 spaces it is more reliable, too.
+    prefs['indent_size'] = 4
+
+    # Builtin and c-extension modules that are allowed to be imported
+    # and inspected by rope.
+    prefs['extension_modules'] = []
+
+    # Add all standard c-extensions to extension_modules list.
+    prefs['import_dynload_stdmods'] = True
+
+    # If `True` modules with syntax errors are considered to be empty.
+    # The default value is `False`; When `False` syntax errors raise
+    # `rope.base.exceptions.ModuleSyntaxError` exception.
+    prefs['ignore_syntax_errors'] = False
+
+    # If `True`, rope ignores unresolvable imports.  Otherwise, they
+    # appear in the importing namespace.
+    prefs['ignore_bad_imports'] = False
+
+    # If `True`, rope will insert new module imports as
+    # `from <package> import <module>` by default.
+    prefs['prefer_module_from_imports'] = False
+
+    # If `True`, rope will transform a comma list of imports into
+    # multiple separate import statements when organizing
+    # imports.
+    prefs['split_imports'] = False
+
+    # If `True`, rope will remove all top-level import statements and
+    # reinsert them at the top of the module when making changes.
+    prefs['pull_imports_to_top'] = True
+
+    # If `True`, rope will sort imports alphabetically by module name instead of
+    # alphabetically by import statement, with from imports after normal
+    # imports.
+    prefs['sort_imports_alphabetically'] = False
+
+    # Location of implementation of rope.base.oi.type_hinting.interfaces.ITypeHintingFactory
+    # In general case, you don't have to change this value, unless you're an rope expert.
+    # Change this value to inject you own implementations of interfaces
+    # listed in module rope.base.oi.type_hinting.providers.interfaces
+    # For example, you can add you own providers for Django Models, or disable the search
+    # type-hinting in a class hierarchy, etc.
+    prefs['type_hinting_factory'] = 'rope.base.oi.type_hinting.factory.default_type_hinting_factory'
+
+
+def project_opened(project):
+    """This function is called after opening the project"""
+    # Do whatever you like here!

MANIFEST.in

@@ -1,5 +1,6 @@
 include bioconda_utils/bioconda_startup.sh
 include bioconda_utils/bioconda_utils-requirements.txt
+include bioconda_utils/bioconda_utils-conda_build_config.yaml
 include bioconda_utils/config.schema.yaml
 include bioconda_utils/channel_order.txt
 include bioconda_utils/templates/*

bioconda_utils/bioconda_utils-conda_build_config.yaml

@@ -0,0 +1,14 @@
+# Additional bioconda-specific pinnings to use in addition to those specified
+# in
+# https://github.com/conda-forge/conda-forge-pinning-feedstock/blob/master/recipe/conda_build_config.yaml
+
+pin_run_as_build:
+  htslib:
+    max_pin: x.x
+  bamtools:
+    max_pin: x.x.x
+
+htslib:
+  - 1.7
+bamtools:
+  - 2.4.1

bioconda_utils/bioconda_utils-requirements.txt

@@ -1,9 +1,9 @@
 anaconda-client=1.6.*
 argh=0.26.*
 beautifulsoup4=4.6.*
-conda=4.3.33
-conda-build=2.1.18
-galaxy-lib>=18.5.5,<18.6.0a0
+conda=4.5.4
+conda-build=3.10.3
+galaxy-lib>=18.5.5
 jinja2=2.10.*
 jsonschema=2.6.*
 networkx=1.11
@@ -21,3 +21,5 @@ colorlog=3.1.*
 six=1.11.*
 alabaster=0.7.*
 git=2.14.*
+conda-forge-pinning=2018.05.22
+python>=3.6

bioconda_utils/bioconductor_skeleton.py

@@ -35,12 +35,6 @@
                    "grid", "methods", "parallel", "splines", "stats", "stats4",
                    "tcltk", "tools", "utils"]
 
-
-# A list of packages, in recipe name format. If a package depends on something
-# in this list, then we will add the gcc/llvm build-deps as appropriate to the
-# constructed recipe.
-GCC_PACKAGES = ['r-rcpp']
-
 HERE = os.path.abspath(os.path.dirname(__file__))
 
 
@@ -594,12 +588,43 @@ def dependencies(self):
             else:
                 dependency_mapping[prefix + name.lower() + version] = name
 
-            if (
-                (prefix + name.lower() in GCC_PACKAGES) or
-                (self.description.get('needscompilation', 'no') == 'yes') or
-                (self.description.get('linkingto', None) is not None)
-            ):
-                self.depends_on_gcc = True
+        if (
+            (self.description.get('needscompilation', 'no') == 'yes') or
+            (self.description.get('linkingto', None) is not None)
+        ):
+            # Modified from conda_build.skeletons.cran
+            #
+            with tarfile.open(self.cached_tarball) as tf:
+                need_f = any([f.name.lower().endswith(('.f', '.f90', '.f77')) for f in tf])
+                need_c = True if need_f else \
+                    any([f.name.lower().endswith('.c') for f in tf])
+                need_cxx = any([f.name.lower().endswith(('.cxx', '.cpp', '.cc', '.c++'))
+                                         for f in tf])
+                need_autotools = any([f.name.lower().endswith('/configure') for f in tf])
+                need_make = True if any((need_autotools, need_f, need_cxx, need_c)) else \
+                    any([f.name.lower().endswith(('/makefile', '/makevars'))
+                        for f in tf])
+        else:
+            need_c = need_cxx = need_f = need_autotools = need_make = False
+
+        for name, version in sorted(versions.items()):
+            if name in ['Rcpp', 'RcppArmadillo']:
+                need_cxx = True
+
+        if need_cxx:
+            need_c = True
+
+        self._cb3_build_reqs = {}
+        if need_c:
+            self._cb3_build_reqs['c'] = "{{ compiler('c') }}"
+        if need_cxx:
+            self._cb3_build_reqs['cxx'] = "{{ compiler('cxx') }}"
+        if need_f:
+            self._cb3_build_reqs['fortran'] = "{{ compiler('fortran') }}"
+        if need_autotools:
+            self._cb3_build_reqs['automake'] = 'automake'
+        if need_make:
+            self._cb3_build_reqs['make'] = 'make'
 
         # Add R itself
         if not specific_r_version:
@@ -721,7 +746,7 @@ def sub_placeholders(x):
                     # object and tries to make a shortcut, causing an error in
                     # decoding unicode. Possible pyaml bug? Anyway, this fixes
                     # it.
-                    ('build', DEPENDENCIES[:]),
+                    ('host', DEPENDENCIES[:]),
                     ('run', DEPENDENCIES[:] + additional_run_deps),
                 )),
             ),
@@ -740,21 +765,25 @@ def sub_placeholders(x):
                 )),
             ),
         ))
-        if self.depends_on_gcc:
-            d['requirements']['build'].append('GCC_PLACEHOLDER')
-            d['requirements']['build'].append('LLVM_PLACEHOLDER')
+
+        if self._cb3_build_reqs:
+            d['requirements']['build'] = []
+        for k, v in self._cb3_build_reqs.items():
+            d['requirements']['build'].append(k + '_' + "PLACEHOLDER")
 
         rendered = pyaml.dumps(d, width=1e6).decode('utf-8')
-        rendered = rendered.replace('GCC_PLACEHOLDER', 'gcc  # [linux]')
-        rendered = rendered.replace('LLVM_PLACEHOLDER', 'llvm  # [osx]')
         rendered = (
             '{% set version = "' + self.version + '" %}\n' +
             '{% set name = "' + self.package + '" %}\n' +
             '{% set bioc = "' + self.bioc_version + '" %}\n\n' +
             rendered
         )
-        tmp = tempfile.NamedTemporaryFile(delete=False).name
-        with open(tmp, 'w') as fout:
+
+        for k, v in self._cb3_build_reqs.items():
+            rendered = rendered.replace(k + '_' + "PLACEHOLDER", v)
+
+        tmpdir = tempfile.mkdtemp()
+        with open(os.path.join(tmpdir, 'meta.yaml'), 'w') as fout:
             fout.write(rendered)
         return fout.name
 
@@ -856,7 +885,6 @@ def write_recipe(package, recipe_dir, config, force=False, bioc_version=None,
         `seen_dependencies`. Only has an effect if `recursive=True`.
     """
     config = utils.load_config(config)
-    env = list(utils.EnvMatrix(config['env_matrix']))[0]
     proj = BioCProjectPage(package, bioc_version, pkg_version)
     logger.info('Making recipe for: {}'.format(package))
 
@@ -895,8 +923,8 @@ def write_recipe(package, recipe_dir, config, force=False, bioc_version=None,
     # *has* changed, then bump the version number.
     meta_file = os.path.join(recipe_dir, 'meta.yaml')
     if os.path.exists(meta_file):
-        updated_meta = utils.load_meta(proj.meta_yaml, env)
-        current_meta = utils.load_meta(meta_file, env)
+        updated_meta = utils.load_first_metadata(proj.meta_yaml).meta
+        current_meta = utils.load_first_metadata(meta_file).meta
 
         # pop off the version and build numbers so we can compare the rest of
         # the dicts