RPACU-52 Parse the "LinkingTo:" field in the DESCRIPTION file

CHANGES.txt

@@ -8,6 +8,7 @@
 - RPACU-50 Switch the license from GPL v2 to Apache 2.0
 - RPACU-51 Check the output messages from stderr and stdout even when
   the R installation command returns a success code
+- RPACU-52 Fix DESCRIPTION file parsing, read the "LinkingTo" field
 
 0.1.9
 -----

README.md

@@ -373,7 +373,10 @@ Downloading R package: tmod_0.30.tar.gz
 Done downloading R package: tmod_0.30.tar.gz
 Package: tmod Version: 0.30 License: GPL (>= 2.0) 
 Repository path: R-3.1.2/tmod_0.30.tar.gz
-Dependencies: beeswarm,pca3d,tagcloud,XML
+Depends: R
+Imports: beeswarm,tagcloud,XML,methods,plotwidgets
+LinkingTo: 
+Suggests: testthat,knitr,rmarkdown,pca3d,limma
 -------------------------------------
 ```
 
@@ -838,9 +841,9 @@ optional arguments:
                         "annotationData". CRAN: "snapshot date".
   --packages PACKAGES   Comma separated list of root packages to create the
                         graph, by default all will be included
-  --traverse TRAVERSE   By default "imports,depends", to traverse both imports
-                        and depends to build the dependency graph. "suggests"
-                        is ignored by default.
+  --traverse TRAVERSE   By default "imports,depends,linkingto", to traverse
+                        all required packages to build the dependency
+                        graph. "suggests" is ignored by default.
   --config CONFIG       RPackUtils configuration file, required unless you use
                         CRAN or Bioconductor as repository
   --out OUT             Output file where to write the GML
@@ -850,9 +853,10 @@ The *--packages* parameter is optional: you can choose to focus on one or
 more particular packages if you like. All available packages in the
 repository will be taken into account otherwise.
 
-You can choose the list of fields from ['imports', 'depends', 'suggests']
-to take into account while building the dependency graph. By default,
-'imports' and 'depends' are used.
+You can choose the list of fields from ['imports', 'depends',
+'linkingto', 'suggests'] to take into account while building the
+dependency graph. By default, 'imports', 'depends' and 'linkingto' are
+used.
 
 Here is an example to compute the dependency graph for all vailable R
 packages from the *2016-05-03* snapshot. This snapshot contains more than
@@ -879,6 +883,7 @@ The gml file has the following attributes for each node:
 | version               | package version                              |
 | depends               | packages in depends                          |
 | imports               | packages in imports                          |
+| linkingto             | packages in linkingto                        |
 | suggests              | packages in suggests                         |
 | license               | package license                              |
 | licenseclass          | ALLOWED / RESTRICETD / BLACKLISTED / UNKNOWN |
@@ -922,10 +927,10 @@ Time elapsed: 22.923 seconds.
 The output file, is a comma-separated format (CSV) and as a table, it looks
 like the following:
 
-| Name     | Version | License            | License class | Depends | Imports         | Suggests                 | Installation allowed | Installation warning |
-|----------|---------|--------------------|---------------|---------|-----------------|--------------------------|----------------------|----------------------|
-| evaluate | 0.9     | MIT + file LICENSE | UNKNOWN       | R       | methods,stringr | testthat,lattice,ggplot2 | True                 | True                 |
-| [...]    |         |                    |               |         |                 |                          |                      |                      |
+| Name     | Version | License            | License class | Depends | Imports         | LinkingTo | Suggests                 | Installation allowed | Installation warning |
+|----------|---------|--------------------|---------------|---------|-----------------|-----------|--------------------------|----------------------|----------------------|
+| evaluate | 0.9     | MIT + file LICENSE | UNKNOWN       | R       | methods,stringr |           | testthat,lattice,ggplot2 | True                 | True                 |
+| [...]    |         |                    |               |         |                 |           |                          |                      |                      |
 
 
 ## Repository types

rpackutils/cli/cliDepsGraph.py

@@ -64,10 +64,10 @@ def rpacks_deps_graph():
         '--traverse',
         dest='traverse',
         action='store',
-        default='imports,depends',
+        default='imports,depends,linkingto',
         required=False,
-        help=('By default \"imports,depends\", to traverse both '
-              'imports and depends to build the dependency graph. '
+        help=('By default \"imports,depends,linkingto\", to traverse all '
+              'required packages to build the dependency graph. '
               '\"suggests\" is ignored by default.'),
     ) and None
     parser.add_argument(
@@ -170,17 +170,19 @@ def rpacks_deps_graph():
        or isinstance(repository, LocalRepository):
         if repoparam is not None:
             logger.warning('Ignoring the --repoparam argument')
-    # traverse options (imports, depends, suggests)
+    # traverse options (imports, depends, suggests, linkingto)
     traverse_imports = ('imports' in traverse)
     traverse_depends = ('depends' in traverse)
     traverse_suggests = ('suggests' in traverse)
+    traverse_linkingto = ('linkingto' in traverse)
     # construct the dependencies tree
     dt = DepTree(repository,
                  lsargs,
                  packinfoargs,
                  traverse_imports,
                  traverse_depends,
-                 traverse_suggests)
+                 traverse_suggests,
+                 traverse_linkingto)
     logger.info('Building the dependencies graph ...')
     dt.build(packagenames=packages)
     if len(dt._g.nodes()) < 2:

rpackutils/cli/cliQuery.py

@@ -99,6 +99,8 @@ def _query_packages(repositories, packages):
                             .format(",".join(packinfo.dependslist)))
                 logger.info('Imports: {}'
                             .format(",".join(packinfo.importslist)))
+                logger.info('LinkingTo: {}'
+                            .format(",".join(packinfo.linkingtolist)))
                 logger.info('Suggests: {}'
                             .format(",".join(packinfo.suggestslist)))
                 # logger.info('Dependencies: {0}' \

rpackutils/cli/cliScan.py

@@ -92,6 +92,7 @@ def _scan_packages(repositories, out):
                     'License class': packinfo.licenseclass,
                     'Depends': ",".join(packinfo.dependslist),
                     'Imports': ",".join(packinfo.importslist),
+                    'LinkingTo': ",".join(packinfo.linkingtolist),
                     'Suggests': ",".join(packinfo.suggestslist),
                     'Installation allowed': packinfo.installation_is_allowed,
                     'Installation warning': packinfo.installation_warning

rpackutils/packinfo.py

@@ -8,7 +8,6 @@
 import tempfile
 import tarfile
 import shutil
-import codecs
 import logging
 from .utils import Utils
 from .rbasepackages import RBasePackages
@@ -65,6 +64,7 @@ def __init__(self, path):
         self.depends = None
         self.imports = None
         self.suggests = None
+        self.linkingto = None
         self.license = None
         self.licenseclass = None
         self.installationisallowed = True
@@ -127,17 +127,21 @@ def dependslist(self):
     def importslist(self):
         return self.imports if self.imports else []
 
+    @property
+    def linkingtolist(self):
+        return self.linkingto if self.linkingto else []
+
     @property
     def suggestslist(self):
         return self.suggests if self.suggests else []
 
     def dependencies(self, withBasePackages=False):
         """
-        Returns an aggregated list of both imports and depends.
+        Returns an aggregated list of imports, depends and linkingto.
 
         :param withBasepackages: if True, remove all R base packages
         """
-        all = self.importslist + self.dependslist
+        all = self.importslist + self.dependslist + self.linkingtolist
         if not withBasePackages:
             all = [x for x in all if x not in RBasePackages.getnames()]
         return all
@@ -168,6 +172,12 @@ def has_imports(self):
             return False
         return len(self.imports) > 0
 
+    @property
+    def has_linkingto(self):
+        if self.linkingto is None:
+            return False
+        return len(self.linkingto) > 0
+
     @property
     def has_suggests(self):
         if self.suggests is None:
@@ -224,6 +234,7 @@ def _do_parse_descriptionfile(self, descriptionfilepath):
             'depends': None,
             'imports': None,
             'suggests': None,
+            'linkingto': None,
             'version': None,
             'license': None
         }
@@ -232,6 +243,7 @@ def _do_parse_descriptionfile(self, descriptionfilepath):
         self.depends = PackInfo._clean_children(d['depends'])
         self.imports = PackInfo._clean_children(d['imports'])
         self.suggests = PackInfo._clean_children(d['suggests'])
+        self.linkingto = PackInfo._clean_children(d['linkingto'])
         self.version = d['version']
         self.license = d['license']
         # compute the license-class

rpackutils/tree.py

@@ -14,7 +14,7 @@ class DepTree(object):
     # FUTURE: we could use multiple providers instead of a single one
     # in order ot search across several repositories
     def __init__(self, provider, lsargs=None, packinfoargs=None,
-                 imports=True, depends=True, suggests=False):
+                 imports=True, depends=True, suggests=False, linkingto=True):
         """
         Traverse Imports and Depends to build the dependency graph
         and ignores Suggests.
@@ -27,6 +27,7 @@ def __init__(self, provider, lsargs=None, packinfoargs=None,
         :param imports: traverse imports
         :param depends: traverse depends
         :param suggests: traverse suggests
+        :param linkingto: traverse linkingto
         """
         self._g = nx.Graph()
         self.excludes = copy.deepcopy(RBasePackages.getnames())
@@ -38,6 +39,7 @@ def __init__(self, provider, lsargs=None, packinfoargs=None,
         self.imports = imports
         self.depends = depends
         self.suggests = suggests
+        self.linkingto = linkingto
 
     def build(self, packagenames=None):
         """
@@ -89,6 +91,12 @@ def _add_node(self, packagename):
                         continue
                     self._add_node(sug_name)
                     self._connect(packinfo.name, sug_name, "suggests")
+            if self.linkingto and packinfo.has_linkingto:
+                for lt_name in packinfo.linkingto:
+                    if lt_name in self.excludes:
+                        continue
+                    self._add_node(lt_name)
+                    self._connect(packinfo.name, lt_name, "linkingto")
 
     def _add_to_graph(self, packinfo):
         self._g.add_node(packinfo.name, **packinfo.as_dict)

tests/resources/bindrcpp/DESCRIPTION

@@ -0,0 +1,26 @@
+Package: bindrcpp
+Title: An 'Rcpp' Interface to Active Bindings
+Version: 0.2.2.9000
+Date: 2018-03-29
+Authors@R: c(
+    person("Kirill", "M\u00fcller", role = c("aut", "cre"), email = "krlmlr+r@mailbox.org", comment = c(ORCID = "0000-0002-1416-3412")),
+    person("RStudio", role = "cph")
+    )
+Description: Provides an easy way to fill an environment with active bindings
+    that call a C++ function.
+License: MIT + file LICENSE
+URL: https://github.com/krlmlr/bindrcpp, https://krlmlr.github.io/bindrcpp
+BugReports: https://github.com/krlmlr/bindrcpp/issues
+Imports: 
+    bindr (>= 0.1.1),
+    Rcpp (>= 0.12.16)
+Suggests: 
+    testthat
+LinkingTo: 
+    plogr,
+    Rcpp
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 6.0.1.9000
+

tests/test_artifactory.py

@@ -48,6 +48,7 @@ def __init__(self, path):
         self.repos = None
         self.depends = None
         self.imports = None
+        self.linkingto = None
         self.suggests = None
         self.license = None
 

tests/test_depsmanager.py

@@ -43,6 +43,7 @@ def __init__(self, name, status):
         self.repos = None
         self.depends = None
         self.imports = None
+        self.linkingto = None
         self.suggests = None
         self.license = None
         self.packagepath = None

tests/test_packinfo.py

@@ -150,3 +150,18 @@ def test__parse_license():
     assert(pi.suggests == ['Rtoto', 'Rtiti', 'Rtata'])
     assert(pi.license == 'AGPL-3 | file LICENSE')
     assert(pi.installationisallowed is False)
+
+
+def test__parse_linkingto():
+    path = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)),
+        'resources',
+        'bindrcpp')
+    pi = PackInfo(path)
+    print(pi.as_dict)
+    assert(pi.name == 'bindrcpp')
+    assert(pi.version == '0.2.2.9000')
+    assert(pi.imports == ['bindr', 'Rcpp'])
+    assert(pi.suggests == ['testthat'])
+    assert(pi.linkingto == ['plogr', 'Rcpp'])
+    assert(pi.license == 'MIT + file LICENSE')