Catch FileNotFoundError when looking for TODO comments

Fixes #796 Also switched the log message from error to critical when halting linting due to failed tests.
nf-core · Dec 3, 2020 · 3be12d4 · 3be12d4
1 parent 8ae626a
commit 3be12d4
Showing 1 changed file with 28 additions and 42 deletions.
diff --git a/nf_core/lint.py b/nf_core/lint.py
@@ -239,7 +239,7 @@ def lint_pipeline(self, release_mode=False):
                 log.debug("Running lint test: {}".format(fun_name))
                 getattr(self, fun_name)()
                 if len(self.failed) > 0:
-                    log.error("Found test failures in `{}`, halting lint run.".format(fun_name))
+                    log.critical("Found test failures in `{}`, halting lint run.".format(fun_name))
                     break
 
     def check_files_exist(self):
@@ -610,10 +610,7 @@ def check_nextflow_config(self):
                 )
             else:
                 self.warned.append(
-                    (
-                        4,
-                        "Config `manifest.version` should end in `dev`: `{}`".format(self.config["manifest.version"]),
-                    )
+                    (4, "Config `manifest.version` should end in `dev`: `{}`".format(self.config["manifest.version"]),)
                 )
         elif "manifest.version" in self.config:
             if "dev" in self.config["manifest.version"]:
@@ -672,19 +669,11 @@ def check_actions_branch_protection(self):
                     "PIPELINENAME", self.pipeline_name.lower()
                 )
                 if has_name and has_if and has_run:
-                    self.passed.append(
-                        (
-                            5,
-                            "GitHub Actions 'branch' workflow looks good: `{}`".format(fn),
-                        )
-                    )
+                    self.passed.append((5, "GitHub Actions 'branch' workflow looks good: `{}`".format(fn),))
                     break
             else:
                 self.failed.append(
-                    (
-                        5,
-                        "Couldn't find GitHub Actions 'branch' check for PRs to master: `{}`".format(fn),
-                    )
+                    (5, "Couldn't find GitHub Actions 'branch' check for PRs to master: `{}`".format(fn),)
                 )
 
     def check_actions_ci(self):
@@ -703,12 +692,7 @@ def check_actions_ci(self):
                 # NB: YAML dict key 'on' is evaluated to a Python dict key True
                 assert ciwf[True] == expected
             except (AssertionError, KeyError, TypeError):
-                self.failed.append(
-                    (
-                        5,
-                        "GitHub Actions CI is not triggered on expected events: `{}`".format(fn),
-                    )
-                )
+                self.failed.append((5, "GitHub Actions CI is not triggered on expected events: `{}`".format(fn),))
             else:
                 self.passed.append((5, "GitHub Actions CI is triggered on expected events: `{}`".format(fn)))
 
@@ -724,10 +708,7 @@ def check_actions_ci(self):
                     assert any([docker_build_cmd in step["run"] for step in steps if "run" in step.keys()])
                 except (AssertionError, KeyError, TypeError):
                     self.failed.append(
-                        (
-                            5,
-                            "CI is not building the correct docker image. Should be: `{}`".format(docker_build_cmd),
-                        )
+                        (5, "CI is not building the correct docker image. Should be: `{}`".format(docker_build_cmd),)
                     )
                 else:
                     self.passed.append((5, "CI is building the correct docker image: `{}`".format(docker_build_cmd)))
@@ -1241,17 +1222,25 @@ def check_cookiecutter_strings(self):
         num_files = 0
         for fn in list_of_files:
             num_files += 1
-            with io.open(fn, "r", encoding="latin1") as fh:
-                lnum = 0
-                for l in fh:
-                    lnum += 1
-                    cc_matches = re.findall(r"{{\s*cookiecutter[^}]*}}", l)
-                    if len(cc_matches) > 0:
-                        for cc_match in cc_matches:
-                            self.failed.append(
-                                (13, "Found a cookiecutter template string in `{}` L{}: {}".format(fn, lnum, cc_match))
-                            )
-                            num_matches += 1
+            try:
+                with io.open(fn, "r", encoding="latin1") as fh:
+                    lnum = 0
+                    for l in fh:
+                        lnum += 1
+                        cc_matches = re.findall(r"{{\s*cookiecutter[^}]*}}", l)
+                        if len(cc_matches) > 0:
+                            for cc_match in cc_matches:
+                                self.failed.append(
+                                    (
+                                        13,
+                                        "Found a cookiecutter template string in `{}` L{}: {}".format(
+                                            fn, lnum, cc_match
+                                        ),
+                                    )
+                                )
+                                num_matches += 1
+            except FileNotFoundError as e:
+                log.warn("`git ls-files` returned '{}' but could not open it!".format(fn))
         if num_matches == 0:
             self.passed.append((13, "Did not find any cookiecutter template strings ({} files)".format(num_files)))
 
@@ -1332,8 +1321,7 @@ def _s(some_list):
         if len(self.passed) > 0 and show_passed:
             table = Table(style="green", box=rich.box.ROUNDED)
             table.add_column(
-                r"\[✔] {} Test{} Passed".format(len(self.passed), _s(self.passed)),
-                no_wrap=True,
+                r"\[✔] {} Test{} Passed".format(len(self.passed), _s(self.passed)), no_wrap=True,
             )
             table = format_result(self.passed, table)
             console.print(table)
@@ -1349,8 +1337,7 @@ def _s(some_list):
         if len(self.failed) > 0:
             table = Table(style="red", box=rich.box.ROUNDED)
             table.add_column(
-                r"\[✗] {} Test{} Failed".format(len(self.failed), _s(self.failed)),
-                no_wrap=True,
+                r"\[✗] {} Test{} Failed".format(len(self.failed), _s(self.failed)), no_wrap=True,
             )
             table = format_result(self.failed, table)
             console.print(table)
@@ -1360,8 +1347,7 @@ def _s(some_list):
         table = Table(box=rich.box.ROUNDED)
         table.add_column("[bold green]LINT RESULTS SUMMARY".format(len(self.passed)), no_wrap=True)
         table.add_row(
-            r"\[✔] {:>3} Test{} Passed".format(len(self.passed), _s(self.passed)),
-            style="green",
+            r"\[✔] {:>3} Test{} Passed".format(len(self.passed), _s(self.passed)), style="green",
         )
         table.add_row(r"\[!] {:>3} Test Warning{}".format(len(self.warned), _s(self.warned)), style="yellow")
         table.add_row(r"\[✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)), style="red")