Change approach for detecting invalid targets

Initially (7374840), snakemake-check-target only used regular
expressions to detect invalid targets based on the presence of a
MissingRuleException or RuleException in Snakemake's output.  The target
was assumed to be valid if these exceptions weren't found.  If there was
a non-zero exit status for another reason, it bubbled up to the compile
call where it was visible to the user.

33a7c90 (snakemake-check-target: Adjust for upstream output, 2016-09-01)
restricted the invalid target check to calls with an exit status of
zero.  This makes the regular expression check useless because snakemake
should always exit with a non-zero status if a MissingRuleException or
RuleException is thrown.  Due to this change, snakemake-check-target
classified all non-zero exits as invalid and all zero exits as valid.
While this often gives the right answer, it doesn't in cases where the
non-zero exit is unrelated to an invalid target.
2bceb7f (snakemake-check-target: Recognize protected items, 2016-09-05)
addressed one case.

To deal with other cases (such as an ambiguous rule error or a syntax
error in the Snakefile), use the following approach.

* An exit status of zero indicates a valid target.

* A non-zero exit status indicates an invalid target if
  snakemake-all-rules has an exit status of zero.  Otherwise,
  snakemake-all-rules will signal an error and display the Snakemake
  output.

The main downside of this approach is the need to call snakemake twice.
The output of snakmake-all-rules is cached, so this is only the case on
the first call to snakemake-check-target for a given version of a
Snakefile.

1 files changed, 23 insertions, 0 deletions

diff --git a/snakemake-test.el b/snakemake-test.el
index 80b6bcd..19a0b99 100644
--- a/snakemake-test.el
+++ b/snakemake-test.el
@@ -820,6 +820,29 @@ two words"
   (should-not
    (snakemake-with-temp-dir
      (snakemake-check-target "cc_wildcards")))
+  ;; Errors with the Snakefile, like ambiguous rules and syntax
+  ;; errors, should be reported as errors rather than treated as
+  ;; invalid targets.
+  (should-error
+   (snakemake-with-temp-dir
+     (write-region "\ndef incomplete_def:"
+                   nil
+                   "Snakefile"
+                   'append)
+     (snakemake-check-target "aa"))
+   :type 'snakemake-error)
+  (should-error
+   (snakemake-with-temp-dir
+     (write-region "\
+
+rule aa:
+    output: \"aa.ambig.out\"
+    shell: \"echo aa.ambig.content > {output}\""
+                   nil
+                   "Snakefile"
+                   'append)
+     (snakemake-check-target "aa"))
+   :type 'snakemake-error)
   ;; Write-protected targets should be recognized as valid targets
   ;; despite Snakemake throwing an error.
   (should