fix: env file usage after changes to source file handling (inspired by #1233 and #1211).

snakemake/common/__init__.py

@@ -25,6 +25,9 @@
 DYNAMIC_FILL = "__snakemake_dynamic__"
 SNAKEMAKE_SEARCHPATH = str(Path(__file__).parent.parent.parent)
 UUID_NAMESPACE = uuid.uuid5(uuid.NAMESPACE_URL, "https://snakemake.readthedocs.io")
+NOTHING_TO_BE_DONE_MSG = (
+    "Nothing to be done (all requested files are present and up to date)."
+)
 
 ON_WINDOWS = platform.system() == "Windows"
 

snakemake/deployment/containerize.py

@@ -7,6 +7,7 @@
 from snakemake.exceptions import WorkflowError
 from snakemake.deployment import conda
 from snakemake.logging import logger
+from snakemake.sourcecache import LocalSourceFile
 
 
 CONDA_ENV_PATH = "/conda-envs"
@@ -22,7 +23,11 @@ def containerize(workflow):
             "Containerization of conda based workflows is not allowed if any conda env definition contains a wildcard."
         )
 
-    relfile = lambda env: os.path.relpath(env.file, os.getcwd())
+    def relfile(env):
+        if isinstance(env.file, LocalSourceFile):
+            return os.path.relpath(env.file.get_path_or_uri(), os.getcwd())
+        else:
+            return env.file.get_path_or_uri()
 
     envs = sorted(
         set(
@@ -59,11 +64,12 @@ def containerize(workflow):
             "\n".join(map("#   {}".format, env.content.decode().strip().split("\n")))
         )
         get_env_cmds.append("RUN mkdir -p {}".format(prefix))
-        if env.file.startswith("https://"):
-            # get_env_cmds.append("RUN curl -sSL {} > {}".format(env.file, env_target_path))
-            get_env_cmds.append("ADD {} {}".format(env.file, env_target_path))
-        else:
+        if isinstance(env.file, LocalSourceFile):
             get_env_cmds.append("COPY {} {}".format(env_source_path, env_target_path))
+        else:
+            get_env_cmds.append(
+                "ADD {} {}".format(env.file.get_path_or_uri(), env_target_path)
+            )
 
         generate_env_cmds.append(
             "mamba env create --prefix {} --file {} &&".format(prefix, env_target_path)

snakemake/sourcecache.py

@@ -105,6 +105,9 @@ def isabs(self):
     def simplify_path(self):
         return utils.simplify_path(self.path)
 
+    def __fspath__(self):
+        return self.path
+
 
 class LocalGitFile(SourceFile):
     def __init__(

snakemake/workflow.py

@@ -73,6 +73,7 @@
     Scatter,
     Gather,
     smart_join,
+    NOTHING_TO_BE_DONE_MSG,
 )
 from snakemake.utils import simplify_path
 from snakemake.checkpoints import Checkpoint, Checkpoints
@@ -820,7 +821,9 @@ def files(items):
                     )
                 else:
                     logger.info(
-                        "Subworkflow {}: Nothing to be done.".format(subworkflow.name)
+                        "Subworkflow {}: {}".format(
+                            subworkflow.name, NOTHING_TO_BE_DONE_MSG
+                        )
                     )
             if self.subworkflows:
                 logger.info("Executing main workflow.")
@@ -955,7 +958,7 @@ def files(items):
             for env in set(job.conda_env for job in dag.jobs):
                 if env:
                     print(
-                        simplify_path(env.file),
+                        env.file.simplify_path(),
                         env.container_img_url or "",
                         simplify_path(env.path),
                         sep="\t",
@@ -1051,13 +1054,13 @@ def files(items):
                 if self.mode == Mode.default:
                     logger.run_info("\n".join(dag.stats()))
             else:
-                logger.info("Nothing to be done.")
+                logger.info(NOTHING_TO_BE_DONE_MSG)
         else:
             # the dryrun case
             if len(dag):
                 logger.run_info("\n".join(dag.stats()))
             else:
-                logger.info("Nothing to be done.")
+                logger.info(NOTHING_TO_BE_DONE_MSG)
                 return True
             if quiet:
                 # in case of dryrun and quiet, just print above info and exit

tests/common.py

@@ -88,6 +88,7 @@ def run(
     subpath=None,
     no_tmpdir=False,
     check_md5=True,
+    check_results=True,
     cores=3,
     set_pythonpath=True,
     cleanup=True,
@@ -181,42 +182,43 @@ def run(
         assert not success, "expected error on execution"
     else:
         assert success, "expected successful execution"
-        for resultfile in get_expected_files(results_dir):
-            if resultfile in [".gitignore", ".gitkeep"] or not os.path.isfile(
-                os.path.join(results_dir, resultfile)
-            ):
-                # this means tests cannot use directories as output files
-                continue
-            targetfile = join(tmpdir, resultfile)
-            expectedfile = join(results_dir, resultfile)
-
-            if ON_WINDOWS:
-                if os.path.exists(join(results_dir, resultfile + "_WIN")):
-                    continue  # Skip test if a Windows specific file exists
-                if resultfile.endswith("_WIN"):
-                    targetfile = join(tmpdir, resultfile[:-4])
-            elif resultfile.endswith("_WIN"):
-                # Skip win specific result files on Posix platforms
-                continue
-
-            assert os.path.exists(targetfile), 'expected file "{}" not produced'.format(
-                resultfile
-            )
-            if check_md5:
-                md5expected = md5sum(expectedfile, ignore_newlines=ON_WINDOWS)
-                md5target = md5sum(targetfile, ignore_newlines=ON_WINDOWS)
-                if md5target != md5expected:
-                    with open(expectedfile) as expected:
-                        expected_content = expected.read()
-                    with open(targetfile) as target:
-                        content = target.read()
-                    assert (
-                        False
-                    ), "wrong result produced for file '{resultfile}':\n------found------\n{content}\n-----expected-----\n{expected_content}\n-----------------".format(
-                        resultfile=resultfile,
-                        content=content,
-                        expected_content=expected_content,
-                    )
+        if check_results:
+            for resultfile in get_expected_files(results_dir):
+                if resultfile in [".gitignore", ".gitkeep"] or not os.path.isfile(
+                    os.path.join(results_dir, resultfile)
+                ):
+                    # this means tests cannot use directories as output files
+                    continue
+                targetfile = join(tmpdir, resultfile)
+                expectedfile = join(results_dir, resultfile)
+
+                if ON_WINDOWS:
+                    if os.path.exists(join(results_dir, resultfile + "_WIN")):
+                        continue  # Skip test if a Windows specific file exists
+                    if resultfile.endswith("_WIN"):
+                        targetfile = join(tmpdir, resultfile[:-4])
+                elif resultfile.endswith("_WIN"):
+                    # Skip win specific result files on Posix platforms
+                    continue
+
+                assert os.path.exists(
+                    targetfile
+                ), 'expected file "{}" not produced'.format(resultfile)
+                if check_md5:
+                    md5expected = md5sum(expectedfile, ignore_newlines=ON_WINDOWS)
+                    md5target = md5sum(targetfile, ignore_newlines=ON_WINDOWS)
+                    if md5target != md5expected:
+                        with open(expectedfile) as expected:
+                            expected_content = expected.read()
+                        with open(targetfile) as target:
+                            content = target.read()
+                        assert (
+                            False
+                        ), "wrong result produced for file '{resultfile}':\n------found------\n{content}\n-----expected-----\n{expected_content}\n-----------------".format(
+                            resultfile=resultfile,
+                            content=content,
+                            expected_content=expected_content,
+                        )
 
     if not cleanup:
         return tmpdir

tests/tests.py

@@ -409,6 +409,10 @@ def test_conda():
     run(dpath("test_conda"), use_conda=True)
 
 
+def test_conda_list_envs():
+    run(dpath("test_conda"), list_conda_envs=True, check_results=False)
+
+
 def test_upstream_conda():
     run(dpath("test_conda"), use_conda=True, conda_frontend="conda")
 
@@ -1221,6 +1225,11 @@ def test_containerized():
     run(dpath("test_containerized"), use_conda=True, use_singularity=True)
 
 
+@skip_on_windows
+def test_containerize():
+    run(dpath("test_conda"), containerize=True, check_results=False)
+
+
 def test_long_shell():
     run(dpath("test_long_shell"))