Merge pull request #56 from aCLImatise/reanalyse

Reanalyse

Author: multimeric

.github/workflows/build.yml

@@ -114,3 +114,9 @@ jobs:
           publish_dir: docs/_build/html
           publish_branch: gh-pages
           enable_jekyll: false
+
+      - name: Update Basecamp
+        uses: peter-evans/repository-dispatch@v1
+        with:
+          token: ${{ secrets.REPOACCESSTOKEN }}
+          event-type: aclimatise-update

aclimatise/model.py

@@ -18,6 +18,7 @@
 from spacy import tokens
 from word2number import w2n
 
+import aclimatise
 from aclimatise import cli_types
 from aclimatise.cli_types import CliFileSystemType, CliString
 from aclimatise.name_generation import generate_name, segment_string
@@ -82,6 +83,37 @@ def __post_init__(self):
                     self.usage_flag = flag
                     self.named.remove(flag)
 
+    def __getitem__(self, item: str) -> "Command":
+        """
+        If present, returns a subcommand with the following name. For example, samtools_cmd['sort'] will return the
+        "samtools sort" command
+        """
+        for sub in self.subcommands:
+            if sub.command == [*self.command, item]:
+                return sub
+        raise KeyError(
+            "{} does not have a subcommand {}".format(" ".join(self.command), item)
+        )
+
+    def reanalyse(self, parent: "Command" = None) -> "Command":
+        """
+        Re-analyses the entire command tree using the existing help text but the current parser, and returns the new tree
+        """
+        if len(self.subcommands) > 0:
+            return Command(
+                generated_using=self.generated_using,
+                help_text=self.help_text,
+                command=self.command,
+                subcommands=[cmd.reanalyse(self) for cmd in self.subcommands],
+                parent=parent,
+            )
+        else:
+            replacement = aclimatise.parse_help(cmd=self.command, text=self.help_text)
+            replacement.parent = parent
+            replacement.help_text = self.help_text
+            replacement.generated_using = self.generated_using
+            return replacement
+
     @property
     def outputs(self) -> typing.List["CliArgument"]:
         """

docs/changes.rst

@@ -1,5 +1,10 @@
 Changelog
 =========
+2.2.0 (2020-09-26)
+------------------
+* Add ``command.reanalyse()``, which re-analyses the help text stored in the command, using the current parser
+* Add ``command['sort']`` which lets you access subcommands by name
+
 2.1.0 (2020-09-22)
 ----------------
 * Add `bedtools random` as a test case

test/test_model.py

@@ -0,0 +1,14 @@
+from aclimatise.model import Command
+
+
+def test_reanalyse(samtools_cmd: Command):
+    """
+    Test the command.reanalyse() method
+    """
+    reanalysed = samtools_cmd.reanalyse()
+    assert reanalysed.help_text == samtools_cmd.help_text
+    assert len(reanalysed.subcommands) == len(samtools_cmd.subcommands)
+
+    re_sort = reanalysed["sort"]
+    assert len(re_sort.positional) > 0
+    assert len(re_sort.named) > 0