Update flow for signac 1.8.0

.circleci/config.yml

@@ -57,30 +57,12 @@ jobs:
           path: test-reports
           destination: test-reports
 
-  linux-python-310-signac-16:
-    <<: *test-template
-    environment:
-      DEPENDENCIES: "NEWEST"
-      SIGNAC_VERSION: "signac~=1.6.0"
-      PYTHON: python
-  linux-python-310-signac-15:
-    <<: *test-template
-    environment:
-      DEPENDENCIES: "NEWEST"
-      SIGNAC_VERSION: "signac~=1.5.0"
-      PYTHON: python
   linux-python-310-signac-latest:
     <<: *test-template
     environment:
       DEPENDENCIES: "NEWEST"
       SIGNAC_VERSION: "git+ssh://git@github.com/glotzerlab/signac.git"
       PYTHON: python
-  linux-python-310-signac-next:
-    <<: *test-template
-    environment:
-      DEPENDENCIES: "NEWEST"
-      SIGNAC_VERSION: "git+ssh://git@github.com/glotzerlab/signac.git@next"
-      PYTHON: python
   linux-python-39:
     <<: *test-template
     docker:
@@ -95,7 +77,7 @@ jobs:
       - image: cimg/python:3.8
     environment:
       DEPENDENCIES: "OLDEST"
-      SIGNAC_VERSION: "signac==1.3.0"
+      SIGNAC_VERSION: "signac==1.8.0"
       PYTHON: python
 
   test-install-pip-python-310: &test-install-pip
@@ -225,16 +207,6 @@ workflows:
       - linux-python-38-oldest:
           post-steps:
             - codecov/upload
-      - linux-python-310-signac-16:
-          requires:
-            - linux-python-310
-          post-steps:
-            - codecov/upload
-      - linux-python-310-signac-15:
-          requires:
-            - linux-python-310
-          post-steps:
-            - codecov/upload
       - check-metadata:
           filters:
             branches:
@@ -248,8 +220,6 @@ workflows:
             - linux-python-39
             - linux-python-38
             - linux-python-38-oldest
-            - linux-python-310-signac-16
-            - linux-python-310-signac-15
   nightly:
     triggers:
       - schedule:
@@ -260,7 +230,6 @@ workflows:
                 - master
     jobs:
       - linux-python-310-signac-latest
-#     - linux-python-310-signac-next
       - test-install-pip-python-310
       - test-install-pip-python-39
       - test-install-pip-python-38

changelog.txt

@@ -10,6 +10,12 @@ Version 0.23
 
 [0.23.0] -- 20xx-xx-xx
 
+Changed
++++++++
+
+- Require ``signac`` version 1.8.0 (#693).
+- Deprecated ``alias`` CLI argument to ``flow init`` (#693).
+
 Fixed
 +++++
 

doc/doc-project.py

@@ -6,4 +6,4 @@ class DocumentationProject(flow.FlowProject):
 
 
 if __name__ == "__main__":
-    DocumentationProject.init_project("DocumentationProject").main()
+    DocumentationProject.init_project().main()

flow/__main__.py

@@ -19,6 +19,7 @@
 from signac import get_project, init_project
 
 from . import __version__, environment, template
+from .util.misc import _deprecated_warning
 
 logger = logging.getLogger(__name__)
 
@@ -28,22 +29,20 @@ def main_init(args):
 
     The available templates are defined in the template module.
     """
-    if not args.alias.isidentifier():
-        raise ValueError(
-            "The alias '{}' is not a valid Python identifier and can therefore "
-            "not be used as a FlowProject alias.".format(args.alias)
-        )
     try:
         get_project()
     except LookupError:
-        init_project(name=args.alias)
-        print(
-            "Initialized signac project with name '{}' in "
-            "current directory.".format(args.alias),
-            file=sys.stderr,
-        )
+        if args.alias != "":
+            _deprecated_warning(
+                deprecation="alias",
+                alternative="",
+                deprecated_in="0.23.0",
+                removed_in="0.24.0",
+            )
+        init_project()
+        print("Initialized signac project in current directory.", file=sys.stderr)
     try:
-        return template.init(alias=args.alias, template=args.template)
+        return template.init(template=args.template)
     except OSError as error:
         raise RuntimeError(
             f"Error occurred while trying to initialize a flow project: {error}"
@@ -120,11 +119,8 @@ def main():
         "alias",
         type=str,
         nargs="?",
-        default="project",
-        help="Name of the FlowProject module to initialize. "
-        "This name will also be used to initialize a signac project if "
-        "no signac project was initialized prior to calling 'init'. "
-        "Default value: 'project'.",
+        default="",
+        help="Unused, will be removed in flow 0.24.0.",
     )
     parser_init.add_argument(
         "-t",

flow/project.py

@@ -89,7 +89,7 @@
 {template_dir}
 
 All template variables can be placed within a template using the standard jinja2
-syntax, e.g., the project root directory can be written as: {{{{ project.root_directory() }}}}.
+syntax, e.g., the project root directory can be written as: {{{{ project.path }}}}.
 The available template variables are:
 {template_vars}
 
@@ -984,9 +984,8 @@ def _generate_id(self, aggregate, operation_name=None):
         else:
             op_string = operation_name
 
-        root_directory = project.root_directory()
         aggregate_id = get_aggregate_id(aggregate)
-        full_name = f"{root_directory}%{aggregate_id}%{op_string}"
+        full_name = f"{project.path}%{aggregate_id}%{op_string}"
         # The job_op_id is a hash computed from the unique full name.
         job_op_id = md5(full_name.encode("utf-8")).hexdigest()
 
@@ -1569,7 +1568,7 @@ def decorated(*jobs):
                     with jobs[0] as job:
                         if getattr(func, "_flow_cmd", False):
                             return (
-                                f'trap "cd $(pwd)" EXIT && cd {job.ws} && {func(job)}'
+                                f'trap "cd $(pwd)" EXIT && cd {job.path} && {func(job)}'
                             )
                         else:
                             return func(job)
@@ -1761,7 +1760,7 @@ def __init__(self, config=None, environment=None, entrypoint=None):
         # the project root directory. This directory may be specified with the 'template_dir'
         # configuration variable.
         self._template_dir = os.path.join(
-            self.root_directory(), self._config.get("template_dir", "templates")
+            self.path, self._config.get("template_dir", "templates")
         )
         self._template_environment_ = {}
 
@@ -2134,7 +2133,7 @@ def _alias(cls, name):
 
     def _fn_bundle(self, bundle_id):
         """Return the canonical name to store bundle information."""
-        return os.path.join(self.root_directory(), ".bundles", bundle_id)
+        return os.path.join(self.path, ".bundles", bundle_id)
 
     def _store_bundled(self, operations):
         """Store operation-ids as part of a bundle and return bundle id.
@@ -4838,7 +4837,7 @@ def _main_run(self, args):
 
         if args.switch_to_project_root:
             with _add_cwd_to_environment_pythonpath():
-                with _switch_to_directory(self.root_directory()):
+                with _switch_to_directory(self.path):
                     run()
         else:
             run()

flow/template.py

@@ -18,13 +18,13 @@
 
 TEMPLATES = {
     "minimal": [
-        ("{alias}.py", "project_minimal.pyt"),
+        ("project.py", "project_minimal.pyt"),
     ],
     "example": [
-        ("{alias}.py", "project_example.pyt"),
+        ("project.py", "project_example.pyt"),
     ],
     "testing": [
-        ("{alias}.py", "project_testing.pyt"),
+        ("project.py", "project_testing.pyt"),
     ],
 }
 

requirements.txt

@@ -1,4 +1,4 @@
-signac>=1.3.0
+signac>=1.8.0
 jinja2>=3.0.0
 cloudpickle>=1.6.0
 deprecation>=2.0.0

setup.py

@@ -7,7 +7,7 @@
 
 requirements = [
     # The core package.
-    "signac>=1.3.0",
+    "signac>=1.8.0",
     # For the templated generation of (submission) scripts.
     "jinja2>=3.0.0",
     # To enable the parallelized execution of operations across processes.

tests/conftest.py

@@ -90,9 +90,7 @@ def setUp(self, request):
         MockScheduler.reset()
         self._tmp_dir = tempfile.TemporaryDirectory(prefix="signac-flow_")
         request.addfinalizer(self._tmp_dir.cleanup)
-        self.project = self.project_class.init_project(
-            name="FlowTestProject", root=self._tmp_dir.name
-        )
+        self.project = self.project_class.init_project(root=self._tmp_dir.name)
         self.cwd = os.getcwd()
 
     def switch_to_cwd(self):
@@ -134,7 +132,7 @@ def call_subcmd(self, subcmd, stderr=subprocess.DEVNULL):
         _cmd = f"python {fn_script} {subcmd}"
         try:
             with _add_path_to_environment_pythonpath(os.path.abspath(self.cwd)):
-                with _switch_to_directory(self.project.root_directory()):
+                with _switch_to_directory(self.project.path):
                     return subprocess.check_output(_cmd.split(), stderr=stderr)
         except subprocess.CalledProcessError as error:
             print(error, file=sys.stderr)

tests/define_status_test_project.py

@@ -39,7 +39,7 @@ def b_is_even(job):
 @_TestProject.pre(b_is_even)
 @_TestProject.post.isfile("world.txt")
 def op1(job):
-    return f'echo "hello" > {job.ws}/world.txt'
+    return f'echo "hello" > {job.path}/world.txt'
 
 
 @group1

tests/define_test_project.py

@@ -48,7 +48,7 @@ def b_is_even(job):
 @_TestProject.pre(b_is_even)
 @_TestProject.post.isfile("world.txt")
 def op1(job):
-    return f'echo "hello" > {job.ws}/world.txt'
+    return f'echo "hello" > {job.path}/world.txt'
 
 
 def _need_to_fork(job):

tests/extract_status.py

@@ -24,7 +24,7 @@ def main(args):
     else:
         return
 
-    p = signac.init_project(name=gen.STATUS_OPTIONS_PROJECT_NAME, root=PROJECT_DIR)
+    p = signac.init_project(root=PROJECT_DIR)
     p.import_from(origin=gen.ARCHIVE_PATH)
 
 

tests/extract_templates.py

@@ -24,7 +24,7 @@ def main(args):
     else:
         return
 
-    p = signac.init_project(name=gen.PROJECT_NAME, root=PROJECT_DIR)
+    p = signac.init_project(root=PROJECT_DIR)
     p.import_from(origin=gen.ARCHIVE_DIR)
 
 

tests/generate_status_reference_data.py

@@ -75,7 +75,7 @@ def main(args):
     ) as status_pr:
         init(p)
         init_status_options(status_pr)
-        fp = _TestProject.get_project(root=p.root_directory())
+        fp = _TestProject.get_project(root=p.path)
         env = flow.environment.TestEnvironment
         # We need to set the scheduler manually. The FakeScheduler
         # won't try to call any cluster executable (e.g. squeue)

tests/generate_template_reference_data.py

@@ -172,11 +172,11 @@ def _store_bundled(self, operations):
 def get_masked_flowproject(p, environment=None):
     """Mock environment-dependent attributes and functions. Need to mock
     sys.executable before the FlowProject is instantiated, and then modify the
-    root_directory and project_dir elements after creation."""
+    path and project_dir elements after creation."""
     try:
         old_executable = sys.executable
         sys.executable = MOCK_EXECUTABLE
-        fp = TestProject.get_project(root=p.root_directory())
+        fp = TestProject.get_project(root=p.path)
         if environment is not None:
             fp._environment = environment
         fp._entrypoint.setdefault("path", "generate_template_reference_data.py")
@@ -190,10 +190,10 @@ def wrapped_generate_id(self, aggregate, *args, **kwargs):
             mocking has to happen within this method to avoid affecting other
             methods called during the test that access the project root directory.
             """
-            old_root_directory = fp.root_directory
-            fp.root_directory = lambda: PROJECT_DIRECTORY
+            old_path = fp.path
+            fp._path = PROJECT_DIRECTORY
             operation_id = old_generate_id(self, aggregate, *args, **kwargs)
-            fp.root_directory = old_root_directory
+            fp._path = old_path
             return operation_id
 
         flow.project.FlowGroup._generate_id = wrapped_generate_id

tests/interactive_template_test.py

@@ -80,7 +80,7 @@ class Project(flow.FlowProject):
     with signac.TemporaryProject() as tmp_project:
         for i in range(num_jobs):
             tmp_project.open_job(dict(foo=i)).init()
-        flow_project = Project.get_project(root=tmp_project.root_directory())
+        flow_project = Project.get_project(root=tmp_project.path)
         flow_project._entrypoint.setdefault("path", entrypoint)
 
         partition = ""

tests/test_directives.py

@@ -321,7 +321,7 @@ def test_evaluate_directive_valid_job(
         self, available_directives_list, non_default_directive_values
     ):
         _tmp_dir = TemporaryDirectory(prefix="flow-directives_")
-        FlowProject.init_project(name="DirectivesTest", root=_tmp_dir.name)
+        FlowProject.init_project(root=_tmp_dir.name)
         project = FlowProject.get_project(root=_tmp_dir.name)
         for i in range(5):
             project.open_job(dict(i=i)).init()

tests/test_project.py

@@ -55,7 +55,7 @@ def setup_project_subprocess_execution(project, stderr_output=sys.stderr):
     Optionally capture stderr with a passed in output or by default output to stderr like normal.
     """
     with _add_cwd_to_environment_pythonpath(), _switch_to_directory(
-        project.root_directory()
+        project.path
     ), redirect_stderr(stderr_output):
         yield
 
@@ -349,7 +349,7 @@ class A(FlowProject):
 
         @A.operation(with_job=True)
         def test_context(job):
-            assert os.path.realpath(os.getcwd()) == os.path.realpath(job.ws)
+            assert os.path.realpath(os.getcwd()) == os.path.realpath(job.path)
 
         project = self.mock_project(A)
         with setup_project_subprocess_execution(project):
@@ -2297,7 +2297,7 @@ def call_subcmd(self, subcmd, stderr=subprocess.DEVNULL):
         _cmd = f"python {fn_script} {subcmd} --debug"
         with _add_path_to_environment_pythonpath(os.path.abspath(self.cwd)):
             try:
-                with _switch_to_directory(self.project.root_directory()):
+                with _switch_to_directory(self.project.path):
                     return subprocess.check_output(_cmd.split(), stderr=stderr)
             except subprocess.CalledProcessError as error:
                 print(error, file=sys.stderr)
@@ -2452,7 +2452,7 @@ def call_subcmd(self, subcmd, stderr=subprocess.STDOUT):
         _cmd = f"python {fn_script} {subcmd} --debug"
         with _add_path_to_environment_pythonpath(os.path.abspath(self.cwd)):
             try:
-                with _switch_to_directory(self.project.root_directory()):
+                with _switch_to_directory(self.project.path):
                     return subprocess.check_output(_cmd.split(), stderr=stderr)
             except subprocess.CalledProcessError as error:
                 return str(error.output)