RF: Read base_packages list from release.yml, and add to manifest files

manifest_rules/__init__.py

 #!/usr/bin/env python
 
 
-__version__ = '0.4.11'
+__version__ = '0.5.0'

manifest_rules/generate_manifest_file.py

@@ -167,9 +167,10 @@ def generate_version_section(version,
         version, platform, cuda = parse_environment_file_name(envfile)
 
         build = {
-            'platform'    : platform,
-            'environment' : url,
-            'sha256'      : checksum
+            'platform'      : platform,
+            'environment'   : url,
+            'sha256'        : checksum,
+            'base_packages' : release_info['base_packages']
         }
         if cuda is not None:
             build['cuda'] = cuda

manifest_rules/test_environment.py

@@ -67,6 +67,7 @@ def full_test(envfile, release_info):
 
     platform      = parse_environment_file_name(envfile)[1]
     miniconda_url = release_info['miniconda'][platform]
+    base_packages = release_info['base_packages']
 
     download_file(miniconda_url, 'miniconda.sh')
 
@@ -74,21 +75,24 @@ def full_test(envfile, release_info):
 
     preprocess_environment(envfile, 'fsl', True)
 
-    basever = None
+    basepkgs = {}
     with open(envfile, 'rt') as f:
         for line in f:
-            if line.strip().startswith('- fsl-base'):
-                basever = line.strip().split()[2]
-                break
+            for pkg in base_packages:
+                if line.strip().startswith(f'- {pkg}'):
+                    pkgver        = line.strip().split(maxsplit=2)[2]
+                    basepkgs[pkg] = pkgver.replace(' ', '=')
 
-    env = os.environ.copy()
+    env            = os.environ.copy()
     env['CONDARC'] = op.abspath(op.join('fsl', 'condarc'))
 
-    if basever is None:
+    if len(basepkgs) == 0:
         env_out = ''
     else:
-        env_out = sprun(f'./fsl/bin/conda install -y '
-                        f'-n base fsl-base={basever}')
+        basepkgs = [f'{pkg}={ver}' for pkg, ver in basepkgs.items()]
+        basepkgs = ' '.join(basepkgs)
+        env_out  = sprun(f'./fsl/bin/conda install -y -n base {basepkgs}',
+                         env=env)
 
     env_out += sprun(f'./fsl/bin/conda env update -n base -f {envfile}',
                      env=env)