hpcflow-new2 0.2.0a185__py3-none-any.whl → 0.2.0a187__py3-none-any.whl

hpcflow/_version.py

@@ -1 +1 @@
-__version__ = "0.2.0a185"
+__version__ = "0.2.0a187"

hpcflow/data/template_components/command_files.yaml

@@ -1,19 +1,26 @@
 - label: t1_infile_1
   name:
     name: t1_infile_1.txt
+  doc: Input file for demonstration task t1.
 - label: t1_infile_2
   name:
     name: t1_infile_2.txt
+  doc: Input file for demonstration task t1.
 - label: t1_outfile_1
   name:
     name: outfile.txt
+  doc: Output file for demonstration task t1.
 - label: lammps_atoms_file
   name:
     name: atoms.lammps
+  doc: The file of atoms processed by LAMMPS.
 - label: lammps_input_script
   name:
     name: in.lammps
+  doc: The LAMMPS control file.
 - label: lammps_dump_files
   name:
     name: (dump.\d+.txt)
     is_regex: true
+  doc: >
+    A regular expression pattern that matches all the dump files generated by a LAMMPS run.

hpcflow/data/template_components/environments.yaml

@@ -1,4 +1,5 @@
 - name: null_env
+  doc: The default system environment.
 
 - name: python_env
   executables:
@@ -7,3 +8,6 @@
         - command: python <<script_name>> <<args>>
           num_cores: 1
           parallel_mode: null
+  doc: |
+    An environment for running Python, typically with access to hpcflow and matflow modules and their dependencies.
+    May be a Python virtual environment.

hpcflow/data/template_components/parameters.yaml

@@ -1,3 +1,4 @@
+# These are only documented when their schemas are documented.
 - type: p1
 - type: p1c
 - type: p2

hpcflow/data/template_components/task_schemas.yaml

@@ -1,4 +1,7 @@
 - objective: test_t1_bash
+  doc: >
+    Simple echo test using bash.
+    <code>p1</code> &rarr; <code>p2</code>
   inputs:
     - parameter: p1
   outputs:
@@ -13,6 +16,9 @@
           stdout: <<parameter:p2>>
 
 - objective: test_t1_ps
+  doc: >
+    Simple echo test using powershell.
+    <code>p1</code> &rarr; <code>p2</code>
   inputs:
     - parameter: p1
   outputs:
@@ -27,6 +33,9 @@
           stdout: <<parameter:p2>>
 
 - objective: test_t1_conditional_OS
+  doc: >
+    Simple echo test showing conditional enactment schemes.
+    <code>p1</code> &rarr; <code>p2</code>
   inputs:
     - parameter: p1
   outputs:
@@ -54,6 +63,9 @@
           stdout: <<parameter:p2>>
 
 - objective: test_t2_bash
+  doc: >
+    Simple echo test using bash.
+    <code>p2</code> &rarr; <code>p3</code>
   inputs:
     - parameter: p2
   outputs:
@@ -68,6 +80,9 @@
           stdout: <<parameter:p3>>
 
 - objective: test_t2_ps
+  doc: >
+    Simple echo test using powershell.
+    <code>p2</code> &rarr; <code>p3</code>
   inputs:
     - parameter: p2
   outputs:
@@ -100,6 +115,9 @@
 #           from_files: [t1_outfile_1]
 
 - objective: dummy_task_1
+  doc: >
+    A dummy task showing simple output file parsing.
+    <code>(p1, p2, p5)</code> &rarr; <code>p3</code>
   inputs:
     - parameter: p1
     - parameter: p2
@@ -119,6 +137,9 @@
           from_files: [t1_outfile_1]
 
 - objective: dummy_task_2
+  doc: >
+    A dummy task showing simple output file parsing.
+    <code>(p3, orientations)</code> &rarr; <code>p4</code>
   inputs:
     - parameter: p3
     - parameter: orientations

hpcflow/sdk/core/command_files.py

@@ -32,6 +32,8 @@ class FileSpec(JSONLike):
     label: str
     #: The name of the file.
     name: str
+    #: Documentation for the file specification.
+    doc: str = ""
     _hash_value: Optional[str] = field(default=None, repr=False)
 
     def __post_init__(self):
@@ -66,6 +68,17 @@ class FileSpec(JSONLike):
         """
         return self.name.ext
 
+    @property
+    def documentation(self) -> str:
+        """
+        Documentation for rendering via Jinja.
+        """
+        if self.doc:
+            import markupsafe
+
+            return markupsafe.Markup(self.doc)
+        return repr(self)
+
 
 class FileNameSpec(JSONLike):
     """

hpcflow/sdk/core/environment.py

@@ -211,10 +211,18 @@ class Environment(JSONLike):
     )
 
     def __init__(
-        self, name, setup=None, specifiers=None, executables=None, _hash_value=None
+        self,
+        name,
+        setup=None,
+        specifiers=None,
+        executables=None,
+        doc="",
+        _hash_value=None,
     ):
         #: The name of the environment.
         self.name = name
+        #: Documentation for the environment.
+        self.doc = doc
         #: Commands to run to enter the environment.
         self.setup = setup
         #: Dictionary of attributes that may be used to supply addional key/value pairs
@@ -257,3 +265,11 @@ class Environment(JSONLike):
                 f"Executables must have unique `label`s within each environment, but "
                 f"found label(s) multiple times: {dup_labels!r}"
             )
+
+    @property
+    def documentation(self) -> str:
+        if self.doc:
+            import markupsafe
+
+            return markupsafe.Markup(self.doc)
+        return repr(self)

hpcflow/sdk/core/task_schema.py

@@ -112,6 +112,7 @@ class TaskSchema(JSONLike):
         parameter_class_modules: Optional[List[str]] = None,
         web_doc: Optional[bool] = True,
         environment_presets: Optional[Dict[str, Dict[str, Dict[str, Any]]]] = None,
+        doc: str = "",
         _hash_value: Optional[str] = None,
     ):
         #: This is a string representing the objective of the task schema.
@@ -133,6 +134,8 @@ class TaskSchema(JSONLike):
         self.web_doc = web_doc
         #: Information about default execution environments.
         self.environment_presets = environment_presets
+        #: Documentation information about the task schema.
+        self.doc = doc
         self._hash_value = _hash_value
 
         self._set_parent_refs()
@@ -589,11 +592,16 @@ class TaskSchema(JSONLike):
             )
             action_show_hide = ""
             act_heading_class = ""
+        description = (
+            f"<h3 class='task-desc'>Description</h3>{self.doc}" if self.doc else ""
+        )
         out = (
-            f"<h5>Inputs</h5>{inputs_table}"
-            f"<h5>Outputs</h5>{outputs_table}"
-            # f"<h5>Examples</h5>examples here..." # TODO:
-            f"<h5{act_heading_class}>Actions{action_show_hide}</h5>{action_table}"
+            f"{description}"
+            f"<h3>Inputs</h3>{inputs_table}"
+            f"<h3>Outputs</h3>{outputs_table}"
+            # f"<h3>Examples</h3>examples here..." # TODO:
+            f"<h3{act_heading_class}>Actions{action_show_hide}</h3>"
+            f"{action_table}"
         )
         return out
 

hpcflow/sdk/core/test_utils.py

@@ -193,9 +193,11 @@ def make_workflow(
     return wk
 
 
-def make_test_data_YAML_workflow(workflow_name, path, **kwargs):
+def make_test_data_YAML_workflow(
+    workflow_name, path, app=None, pkg="hpcflow.tests.data", **kwargs
+):
     """Generate a workflow whose template file is defined in the test data directory."""
-    pkg = "hpcflow.tests.data"
+    app = hf if app is None else app
     try:
         script_ctx = resources.as_file(resources.files(pkg).joinpath(workflow_name))
     except AttributeError:
@@ -203,12 +205,14 @@ def make_test_data_YAML_workflow(workflow_name, path, **kwargs):
         script_ctx = resources.path(pkg, workflow_name)
 
     with script_ctx as file_path:
-        return hf.Workflow.from_YAML_file(YAML_path=file_path, path=path, **kwargs)
+        return app.Workflow.from_YAML_file(YAML_path=file_path, path=path, **kwargs)
 
 
-def make_test_data_YAML_workflow_template(workflow_name, **kwargs):
+def make_test_data_YAML_workflow_template(
+    workflow_name, app=None, pkg="hpcflow.tests.data", **kwargs
+):
     """Generate a workflow template whose file is defined in the test data directory."""
-    pkg = "hpcflow.tests.data"
+    app = hf if app is None else app
     try:
         script_ctx = resources.as_file(resources.files(pkg).joinpath(workflow_name))
     except AttributeError:
@@ -216,7 +220,7 @@ def make_test_data_YAML_workflow_template(workflow_name, **kwargs):
         script_ctx = resources.path(pkg, workflow_name)
 
     with script_ctx as file_path:
-        return hf.WorkflowTemplate.from_file(path=file_path, **kwargs)
+        return app.WorkflowTemplate.from_file(path=file_path, **kwargs)
 
 
 @dataclass

hpcflow/sdk/data/environments_spec_schema.yaml

@@ -2,7 +2,7 @@ rules:
   - path: []
     condition:
       {
-        value.allowed_keys: [name, setup, executables, specifiers, _hash_value],
+        value.allowed_keys: [name, setup, executables, specifiers, doc, _hash_value],
       }
   - path: [setup]
     condition:

hpcflow/sdk/data/files_spec_schema.yaml

@@ -1,5 +1,5 @@
 rules:
   - path: []
-    condition: { value.allowed_keys: [label, name, _hash_value] }
+    condition: { value.allowed_keys: [label, name, doc, _hash_value] }
   - path: [name]
     condition: { value.allowed_keys: [name, args, is_regex] }

{hpcflow_new2-0.2.0a185.dist-info → hpcflow_new2-0.2.0a187.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hpcflow-new2
-Version: 0.2.0a185
+Version: 0.2.0a187
 Summary: Computational workflow management
 License: MIT
 Author: aplowman

{hpcflow_new2-0.2.0a185.dist-info → hpcflow_new2-0.2.0a187.dist-info}/RECORD

@@ -1,7 +1,7 @@
 hpcflow/__init__.py,sha256=WIETuRHeOp2SqUqHUzpjQ-lk9acbYv-6aWOhZPRdlhs,64
 hpcflow/__pyinstaller/__init__.py,sha256=YOzBlPSck6slucv6lJM9K80JtsJWxXRL00cv6tRj3oc,98
 hpcflow/__pyinstaller/hook-hpcflow.py,sha256=SeMopsPkhCyd9gqIrzwFNRj3ZlkUlUYl-74QYz61mo4,1089
-hpcflow/_version.py,sha256=C3p4CSYN9Aj246WMo18k7IpcpZxR_PPEEtdWh9kiVmA,26
+hpcflow/_version.py,sha256=tZjj8d3X3pZKHr9ZyYEM1dJulI_o_IPI6rj5HHMLbUA,26
 hpcflow/app.py,sha256=d-kgfnZNlqlCi2H8bK26714brD_u3ibN3FaEZgjF9aA,1332
 hpcflow/cli.py,sha256=G2J3D9v6MnMWOWMMWK6UEKLn_6wnV9lT_qygEBBxg-I,66
 hpcflow/data/demo_data_manifest/__init__.py,sha256=Hsq0jT8EXM13wu1MpGy5FQgyuz56ygep4VWOnulFn50,41
@@ -27,10 +27,10 @@ hpcflow/data/scripts/main_script_test_json_out_obj.py,sha256=9715rSsbslIB3ZuF22p
 hpcflow/data/scripts/main_script_test_json_sub_param_in_json_out_labels.py,sha256=GkKqWb-A32ahgX5L_uDWZFfjC6IhBOKKGGP34N2O2tA,402
 hpcflow/data/scripts/parse_t1_file_01.py,sha256=2BVotqY3sMc3FXSUPCvnzSHfymyGI9wYYOYrTrXngyI,125
 hpcflow/data/template_components/__init__.py,sha256=qv0IzZGQho4aBR2eld5rNFiYlb8nDcTvkAwa982jDWs,83
-hpcflow/data/template_components/command_files.yaml,sha256=9y82MoHkn6Vgi8V_SQgCWTLm09h5SlfbD8InRoJB3Qo,356
-hpcflow/data/template_components/environments.yaml,sha256=ed__VCjiRWGuX1GSRI7ut2DMeFu-_JnhgSEmLSXp3hY,200
-hpcflow/data/template_components/parameters.yaml,sha256=rJ-3f1GRiNGS6oDV9T1-H_fb1-o29KWn2hovJmDyLas,211
-hpcflow/data/template_components/task_schemas.yaml,sha256=VMtzckqDyfL9JpjYkG9FkzlVGYxaFvPo307Sx6ctVFk,3217
+hpcflow/data/template_components/command_files.yaml,sha256=HmkyqF7ZJL4z6HDx6U2kaxxog22QGHBcxqZ5oQZdPaI,671
+hpcflow/data/template_components/environments.yaml,sha256=OomUuUw1BLNGou-DeGhVwJBKz1nZTGdMJz4JV_g-5pQ,405
+hpcflow/data/template_components/parameters.yaml,sha256=CMmO_2CofWi8OGQ0r9B8pIj4pf1F6LChYOjEuW1KD6U,274
+hpcflow/data/template_components/task_schemas.yaml,sha256=CHMJZ6F9TAvNyhEYTJjmab12cPS8p2iPeWaTPHctNWY,3917
 hpcflow/data/workflows/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 hpcflow/data/workflows/workflow_1.yaml,sha256=lF7Re2SVc_5gQk5AwB0gXaq-n-T5ia4su3zNQ9oMRV0,220
 hpcflow/examples.ipynb,sha256=cLKp4QsxwwMXRanDnfWY9kqsV23q6G4raOpu6IZXnMw,28553
@@ -47,10 +47,10 @@ hpcflow/sdk/config/errors.py,sha256=HpqGJdFlJzFO2B7eRSvTHMySwCUAI-b89YRS1DyZ5As,
 hpcflow/sdk/core/__init__.py,sha256=qcsbBwQNp7HVDzW-HZWg2-J0BAFzU0tJmQP0jKDBR-Q,299
 hpcflow/sdk/core/actions.py,sha256=6gJnwYe3Olmz_FwiH4WvDbb3ffvNkhrByg-FsBGVSCI,90840
 hpcflow/sdk/core/cache.py,sha256=EX1Kx8qrAP_lJpadMgIH72CCJVe-_LWRA-Z1PwfsQPg,5949
-hpcflow/sdk/core/command_files.py,sha256=LMa4eXRLnl4NmOy5mYZkEBy4nWA9Nq6eUew8K_r7RCM,25142
+hpcflow/sdk/core/command_files.py,sha256=O5UlbiOx5slu_1t6WY75LSywNPrydPgHqRqtX-01itc,25456
 hpcflow/sdk/core/commands.py,sha256=xIg82Fw6djuD32a4BwN5WreOlL-K7cUwg5ks8glwodM,14624
 hpcflow/sdk/core/element.py,sha256=EoWP2o6doLL_DjO1_VjK4y6-KyKasAXv_JWszFS7yIE,58150
-hpcflow/sdk/core/environment.py,sha256=IKU1-S6aCl8SBbXzuC2KTpMfzwTfGgNcdu8Hb7eCqz0,7729
+hpcflow/sdk/core/environment.py,sha256=aN3iAllVY5XluyNDRsm52Gv2DqzeEoVNBSODjTZ4ncA,8031
 hpcflow/sdk/core/errors.py,sha256=gcy50oJbjGZzmVKpLl5nUxfJkanw_78bDPi5oQdaMa0,13728
 hpcflow/sdk/core/json_like.py,sha256=opGf5GnQdufrlYZUDI61Sq8FVOWDAIPdFUmmy5ohlbo,21329
 hpcflow/sdk/core/loop.py,sha256=0DEjHiw8xn4S2uPpaucpx2tnkMbETaFwMLnqe_Oye60,34130
@@ -61,8 +61,8 @@ hpcflow/sdk/core/parameters.py,sha256=V4zBIqLuc6lENHoUXTM3bjqRcfRfq-0ay0QuN3WwA5
 hpcflow/sdk/core/rule.py,sha256=cWpGaBiYsRHKeaG1XfbI_Rgwhpz6rfM-sQ1nUeTKKhA,5625
 hpcflow/sdk/core/run_dir_files.py,sha256=wtgWuvtWuNFo5YG5v1k3EBvYQFqGkr27mv4NqMlp4lQ,2410
 hpcflow/sdk/core/task.py,sha256=zwGW-YewQIh9JSDDV5mrm7epPFT0SRT7ofpI2HUh6RM,131822
-hpcflow/sdk/core/task_schema.py,sha256=ORi3iULG7J7JeQu1CaovTzBc4-mP2tthxq6g0JBdDnE,34448
-hpcflow/sdk/core/test_utils.py,sha256=vkpZesJNFNfBxjIDDr_WKIxFx2tUkde_kPn6eDjtwxs,10303
+hpcflow/sdk/core/task_schema.py,sha256=uuV8_2iEZ2Q-0ZMnkdgbUsR6b7KOLrGFG69QD7zE9wQ,34717
+hpcflow/sdk/core/test_utils.py,sha256=_LoTkZj97lZkJ6ijvfWmPjn7tnsK9-h3dOTnE5rAgjs,10401
 hpcflow/sdk/core/utils.py,sha256=9PHfwfUyREJTSQYlCbRbKHwrx1SA6c7Uh_TFrg9xynQ,28591
 hpcflow/sdk/core/validation.py,sha256=jWBJiHOv2_pL-Dua9dpsd6Qc2KmDZOQeVhFri4vMn6U,704
 hpcflow/sdk/core/workflow.py,sha256=nd_NWNPZUgpc4GvX5Ivy1oF__Dj2Q_kIAfvQbBohXjs,120067
@@ -70,8 +70,8 @@ hpcflow/sdk/core/zarr_io.py,sha256=RgJia3jgE3Y16ERU4nWNzHNDkK-qDS1znZMB1IfOUd4,6
 hpcflow/sdk/data/__init__.py,sha256=-YzROirohSKU2UGYj5vkCe_J2KejbzhIjUXNaJwKHLk,568
 hpcflow/sdk/data/config_file_schema.yaml,sha256=7i3z_m3GBRtLyB4c7qPngnlQWqcIq1CyCcOysDyq4es,791
 hpcflow/sdk/data/config_schema.yaml,sha256=FOB7hiWySulWA86ERJKeJjzlNKW_eP4q2hUWpV__TEM,6488
-hpcflow/sdk/data/environments_spec_schema.yaml,sha256=567S6KYkAzeV4eyUCuSpUr8LnsD2BKI7fUZVRxeYtsw,790
-hpcflow/sdk/data/files_spec_schema.yaml,sha256=yNA52Te-6p3a-TzWvrVx_0kEy7ZpJYhrLmgSbZ6UwH8,165
+hpcflow/sdk/data/environments_spec_schema.yaml,sha256=MNNbc49HuATGYdVuItR4sbrvVDvNrADKnvSs3xCYqr0,795
+hpcflow/sdk/data/files_spec_schema.yaml,sha256=kY--Jol4ia55ctzZa8a5ls8SPTdNwgDLoEoYbpP0EYs,170
 hpcflow/sdk/data/parameters_spec_schema.yaml,sha256=Wj7CvG7Ul1nZDtBca-oxeFH_aSZkBSz4oQpnuM7VKls,148
 hpcflow/sdk/data/task_schema_spec_schema.yaml,sha256=6NROg7x-493bdvRwvY4M71R7POT-tNnmROkEsnnoL4k,93
 hpcflow/sdk/data/workflow_spec_schema.yaml,sha256=RjMALO0yAjVvnnp9KjzsSFPLkkRHztiuAHhYiXDGyWM,392
@@ -151,8 +151,8 @@ hpcflow/tests/unit/test_workflow_template.py,sha256=fF7LNveMwCledgncNCRfD9Nd9dL9
 hpcflow/tests/workflows/test_jobscript.py,sha256=9sp1o0g72JZbv2QlOl5v7wCZEFjotxiIKGNUxVaFgaA,724
 hpcflow/tests/workflows/test_workflows.py,sha256=xai6FRtGqG4lStJk6KmsqPUSuvqs9FrsBOxMVALshIs,13400
 hpcflow/viz_demo.ipynb,sha256=1QdnVsk72vihv2L6hOGyk318uEa22ZSgGxQCa7hW2oo,6238
-hpcflow_new2-0.2.0a185.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
-hpcflow_new2-0.2.0a185.dist-info/METADATA,sha256=CMwsBvBMQHXOwYaKyFpSnRSd5svVHA8kkcfewDdVqRU,2465
-hpcflow_new2-0.2.0a185.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-hpcflow_new2-0.2.0a185.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
-hpcflow_new2-0.2.0a185.dist-info/RECORD,,
+hpcflow_new2-0.2.0a187.dist-info/LICENSE,sha256=Xhxf_KsrJNJFGMogumZhXSTPhUOVHCWf7nU-TDzqg0E,16763
+hpcflow_new2-0.2.0a187.dist-info/METADATA,sha256=mctk35qSMCaPv8GpwqWnhI93-p52xBBoMCfkocV-9wM,2465
+hpcflow_new2-0.2.0a187.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+hpcflow_new2-0.2.0a187.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
+hpcflow_new2-0.2.0a187.dist-info/RECORD,,