math-spec-mapping 0.3.15__tar.gz → 0.3.17__tar.gz

{math_spec_mapping-0.3.15/src/math_spec_mapping.egg-info → math_spec_mapping-0.3.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: math-spec-mapping
-Version: 0.3.15
+Version: 0.3.17
 Summary: A library for easy mapping of mathematical specifications.
 Author-email: Sean McOwen <Sean@Block.Science>
 Classifier: Programming Language :: Python :: 3

{math_spec_mapping-0.3.15 → math_spec_mapping-0.3.17}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 [project]
 name = "math-spec-mapping"
-version = "0.3.15"
+version = "0.3.17"
 authors = [
   { name="Sean McOwen", email="Sean@Block.Science" },
 ]

{math_spec_mapping-0.3.15 → math_spec_mapping-0.3.17}/src/math_spec_mapping/Classes/Block.py

@@ -69,7 +69,7 @@ class Block:
 
         self.find_all_spaces_used(data)
 
-    def render_mermaid(self, i):
+    def render_mermaid(self, i, go_deep=True):
         i += 1
         out = 'X{}["{}"]'.format(i, self.name)
         if self.block_type == "Mechanism":
@@ -87,7 +87,7 @@ class Block:
         elif self.block_type in ["Parallel Block", "Stack Block", "Split Block"]:
             updates = self.all_updates
         else:
-            return "\n", {}
+            return "\n", {}, 0
         updates = sorted(updates, key=lambda x: x[0].name + "-" + x[1].name)
 
         out = "\n"
@@ -115,18 +115,30 @@ class Block:
             out += "\n"
         out += "end\n"
         out += "\n"
-        return out, entity_variable_mapping
+        return out, entity_variable_mapping, len(entities)
 
-    def render_mermaid_root(self):
+    def render_mermaid_root(self, go_deep=True):
         out = """```mermaid\ngraph TB\n"""
-        add, entity_variable_mapping = self.render_ending_entities()
+        add, entity_variable_mapping, n_entities = self.render_ending_entities()
         out += add
-        out += self.render_mermaid(0)[0]
+        new, i = self.render_mermaid(0, go_deep=go_deep)
+        out += new
 
         for key in entity_variable_mapping:
             out = out.replace(key, entity_variable_mapping[key])
-        out += "\n```"
+        out += "\n"
+        for x in range(1, i):
+            if (
+                "X{}[Domain]".format(x) not in out
+                and "X{}[Codomain]".format(x) not in out
+                and "subgraph X{}".format(x) not in out
+            ):
+                out += "class X{} internal-link;\n".format(x)
 
+        for x in range(n_entities):
+            out += "class EE{} internal-link;\n".format(x)
+
+        out += "\n```"
         return out
 
     def find_all_spaces_used(self, data):
@@ -223,7 +235,19 @@ class ParallelBlock(Block):
         self.metadata = data["metadata"]
         self.find_all_spaces_used(data)
 
-    def render_mermaid(self, i):
+    def render_mermaid(self, i, go_deep=True):
+        if go_deep == "First":
+            go_deep = False
+        elif go_deep == False:
+            i += 1
+            out = 'X{}["{}"]'.format(i, self.name)
+            for u in self.all_updates:
+                out += "\n"
+                out += "X{} --> {}".format(
+                    i,
+                    (u[0].name + "-" + u[1].name).replace(" ", "-"),
+                )
+            return out, i
         multi = None
         if type(i) == list:
             multi = i
@@ -251,7 +275,7 @@ class ParallelBlock(Block):
                 if x.name not in ["Empty Space", "Terminating Space"]
             ]
 
-            component, i = component.render_mermaid(i)
+            component, i = component.render_mermaid(i, go_deep=go_deep)
             out += component
             out += "\n"
             domain_map[i] = domain
@@ -404,7 +428,19 @@ class StackBlock(Block):
                     )
         return channels
 
-    def render_mermaid(self, i):
+    def render_mermaid(self, i, go_deep=True):
+        if go_deep == "First":
+            go_deep = False
+        elif go_deep == False:
+            i += 1
+            out = 'X{}["{}"]'.format(i, self.name)
+            for u in self.all_updates:
+                out += "\n"
+                out += "X{} --> {}".format(
+                    i,
+                    (u[0].name + "-" + u[1].name).replace(" ", "-"),
+                )
+            return out, i
         multi = None
         if type(i) == list:
             multi = i
@@ -423,7 +459,7 @@ class StackBlock(Block):
                 for x in domain
                 if x.name not in ["Empty Space", "Terminating Space"]
             ]
-            component, i = component.render_mermaid(i)
+            component, i = component.render_mermaid(i, go_deep=go_deep)
             domain_map[i] = domain
             out += component
             out += "\n"
@@ -535,7 +571,7 @@ class SplitBlock(Block):
         self.metadata = data["metadata"]
         self.find_all_spaces_used(data)
 
-    def render_mermaid(self, i):
+    def render_mermaid(self, i, go_deep=True):
         multi = None
         if type(i) == list:
             multi = i

{math_spec_mapping-0.3.15 → math_spec_mapping-0.3.17}/src/math_spec_mapping/Classes/MathSpec.py

@@ -8,7 +8,8 @@ import os
 from copy import deepcopy
 import shutil
 import pandas as pd
-from inspect import signature, getsource
+from inspect import signature, getsource, getfile
+from IPython.display import display, Markdown
 
 
 class MathSpec:
@@ -1116,13 +1117,34 @@ class MathSpecImplementation:
 
     def load_source_files(self):
         self.source_files = {}
-        for key in self.components:
+        self.file_names = {}
+        for key in self.blocks:
             self.source_files[key] = getsource(self.components[key])
+            self.file_names[key] = getfile(self.components[key])
 
-    def print_source_code_files(self, keys=None):
+    def print_source_code_files(self, keys=None, markdown=True):
         if not keys:
             keys = list(self.source_files.keys())
         for key in keys:
+            # Skip wirings
+            if key not in self.ms.components:
+                continue
             print("-" * 20 + key + "-" * 20)
-            print(self.source_files[key])
+            if markdown:
+                display(
+                    Markdown(
+                        """```python
+{}
+```""".format(
+                            self.source_files[key]
+                        )
+                    )
+                )
+            else:
+                print(self.source_files[key])
+            print("\n")
+            full_path = self.file_names[key]
+            print("File path: {}".format(full_path))
+            relative_path = "./" + os.path.relpath(full_path, os.getcwd())
+            print("Relative file path: {}".format(relative_path))
             print("\n\n\n")

math_spec_mapping-0.3.17/src/math_spec_mapping/Convenience/__init__.py

@@ -0,0 +1,8 @@
+# from .documentation import write_top_level_json_description
+from .starter import remove_dummy_repo_components
+from .github import (
+    write_scaffold_to_github_issues,
+    find_open_issues,
+    create_priority_label_matrix,
+    create_milestone_label_matrix,
+)

math_spec_mapping-0.3.17/src/math_spec_mapping/Convenience/github.py

@@ -0,0 +1,108 @@
+import os
+import requests
+from github import Github, Auth
+import pandas as pd
+from dotenv import load_dotenv
+
+
+def write_scaffold_to_github_issues(
+    scaffolder_folder, repo_owner, repository_name, access_token
+):
+    folders = [
+        x
+        for x in os.listdir(scaffolder_folder)
+        if os.path.isdir(scaffolder_folder + "/" + x)
+    ]
+    headers = {
+        "Accept": "application/vnd.github+json",
+        "X-GitHub-Api-Version": "2022-11-28",
+        "Authorization": "Bearer {}".format(access_token),
+    }
+    for folder in folders:
+        issue_name = "Write {} from MSML Scaffold".format(folder)
+        checklist = [
+            x[:-3]
+            for x in os.listdir(scaffolder_folder + "/" + folder)
+            if x.endswith(".md")
+        ]
+        checklist = ["- [ ] " + x for x in checklist]
+        checklist = "\n".join(checklist)
+
+        requests.post(
+            "https://api.github.com/repos/{}/{}/issues".format(
+                repo_owner, repository_name
+            ),
+            headers=headers,
+            json={"title": issue_name, "body": checklist},
+        )
+
+
+def find_open_issues():
+    load_dotenv()
+    g = Github(auth=Auth.Token(os.getenv("GITHUB_TOKEN")))
+    repo = g.get_repo("BlockScience/MSML")
+    open_issues = repo.get_issues(state="open")
+    open_issues = list(open_issues)
+
+    df = pd.DataFrame(
+        [[x.title, x.labels, x.html_url, x.milestone] for x in open_issues],
+        columns=["Name", "Labels", "URL", "Milestone"],
+    )
+    df["Milestone"] = df["Milestone"].apply(lambda x: x.title if x else None)
+    df = df.join(
+        df["Labels"]
+        .apply(lambda x: {y.name: True for y in x})
+        .apply(pd.Series)
+        .fillna(False)
+    )
+
+    empty = df[df["Labels"].apply(lambda x: len(x)) == 0]
+    empty = empty[~empty["URL"].str.contains("MSML/pull")]
+    assert len(empty) == 0, "Some issues do not have labels"
+
+    return df, open_issues
+
+
+def create_priority_label_matrix(df, exclude_milestones=None):
+    if exclude_milestones:
+        df = df[~df["Milestone"].isin(exclude_milestones)]
+    priority_labels = ["High Priority", "Medium Priority", "Low Priority"]
+    labels = list(df.columns[4:])
+    labels = sorted([x for x in labels if x not in priority_labels])
+
+    table = []
+    for label in labels:
+        row = []
+        for priority in priority_labels:
+            row.append(df[(df[priority]) & (df[label])])
+        table.append(row)
+    table = pd.DataFrame(table, index=labels, columns=priority_labels)
+    table = table.applymap(
+        lambda y: "\n".join(
+            y.apply(lambda x: "[{}]({})".format(x["Name"], x["URL"]), axis=1).values
+        )
+    )
+    return table
+
+
+def create_milestone_label_matrix(df, exclude_milestones=None):
+    if exclude_milestones:
+        df = df[~df["Milestone"].isin(exclude_milestones)]
+    priority_labels = ["High Priority", "Medium Priority", "Low Priority"]
+    labels = list(df.columns[4:])
+    labels = sorted([x for x in labels if x not in priority_labels])
+    milestones = sorted(list(df[~pd.isnull(df["Milestone"])]["Milestone"].unique()))
+
+    table = []
+    for label in labels:
+        row = []
+        for milestone in milestones:
+            row.append(df[(df["Milestone"] == milestone) & (df[label])])
+        table.append(row)
+    table = pd.DataFrame(table, index=labels, columns=milestones)
+    table = table.applymap(
+        lambda y: "\n".join(
+            y.apply(lambda x: "[{}]({})".format(x["Name"], x["URL"]), axis=1).values
+        )
+    )
+    return table

{math_spec_mapping-0.3.15 → math_spec_mapping-0.3.17}/src/math_spec_mapping/Reports/markdown.py

@@ -1,5 +1,19 @@
 import os
 from .state import write_state_section
+from inspect import signature, getsource, getfile
+
+
+def get_source_code(ms, component_type, implementation_name):
+    if implementation_name in ms.implementations["python"][component_type]:
+        code = ms.implementations["python"][component_type][implementation_name]
+    else:
+        return None
+    source_code = """```python
+{}```""".format(
+        getsource(code)
+    )
+    file_path = getfile(code)
+    return source_code, file_path
 
 
 def write_entity_markdown_report(ms, path, entity, add_metadata=True):
@@ -179,7 +193,23 @@ def write_boundary_action_markdown_report(ms, path, boundary_action, add_metadat
 
             out += "#### Logic\n"
             out += x.logic
-            out += "\n\n"
+            out += "\n"
+
+            temp = get_source_code(ms, "boundary_action_options", x.name)
+            if temp:
+                source_code, file_path = temp
+                file_path = os.path.relpath(
+                    file_path, "{}/Boundary Actions".format(path)
+                )
+                out += "#### Python Implementation\n"
+                out += source_code
+                out += "\n"
+                out += "Implementation Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+                    file_path, file_path
+                )
+                out += "\n"
+
+            out += "\n"
 
     with open(
         "{}/Boundary Actions/{}.md".format(path, boundary_action.label), "w"
@@ -256,7 +286,21 @@ def write_policy_markdown_report(ms, path, policy, add_metadata=True):
 
             out += "#### Logic\n"
             out += x.logic
-            out += "\n\n"
+            out += "\n"
+
+            temp = get_source_code(ms, "policies", x.name)
+            if temp:
+                source_code, file_path = temp
+                file_path = os.path.relpath(file_path, "{}/Policies".format(path))
+                out += "#### Python Implementation\n"
+                out += source_code
+                out += "\n"
+                out += "Implementation Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+                    file_path, file_path
+                )
+                out += "\n"
+
+            out += "\n"
 
     with open("{}/Policies/{}.md".format(path, policy.label), "w") as f:
         f.write(out)
@@ -323,6 +367,20 @@ def write_mechanism_markdown_report(ms, path, mechanism, add_metadata=True):
         )
         out += "\n"
 
+    temp = get_source_code(ms, "mechanisms", mechanism.name)
+    if temp:
+        source_code, file_path = temp
+        file_path = os.path.relpath(file_path, "{}/Mechanisms".format(path))
+        out += "## Python Implementation\n"
+        out += source_code
+        out += "\n"
+        out += "Implementation Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+            file_path, file_path
+        )
+        out += "\n"
+
+    out += "\n"
+
     with open("{}/Mechanisms/{}.md".format(path, mechanism.label), "w") as f:
         f.write(out)
 
@@ -434,7 +492,23 @@ def write_control_action_markdown_report(ms, path, control_action, add_metadata=
 
             out += "#### Logic\n"
             out += x.logic
-            out += "\n\n"
+            out += "\n"
+
+            temp = get_source_code(ms, "control_action_options", x.name)
+            if temp:
+                source_code, file_path = temp
+                file_path = os.path.relpath(
+                    file_path, "{}/Control Actions".format(path)
+                )
+                out += "#### Python Implementation\n"
+                out += source_code
+                out += "\n"
+                out += "Implementation Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+                    file_path, file_path
+                )
+                out += "\n"
+
+            out += "\n"
 
     with open("{}/Control Actions/{}.md".format(path, control_action.label), "w") as f:
         f.write(out)
@@ -454,6 +528,13 @@ def write_wiring_markdown_report(ms, path, wiring, add_metadata=True):
 """.format(
                 "\n".join(["{}: {}".format(x, metadata[x]) for x in metadata])
             )
+    out += "## Wiring Diagram (Zoomed Out)"
+    out += "\n"
+    out += "\n"
+    out += "- For display of only depth of 1 in the components/nested wirings\n"
+    out += wiring.render_mermaid_root(go_deep="First")
+    out += "\n"
+    out += "\n"
 
     out += "## Wiring Diagram"
     out += "\n"
@@ -707,6 +788,12 @@ def write_state_variables_markdown_reports(ms, path, state, add_metadata=True):
             out += variable.domain
         out += "\n\n"
 
+        out += "Updated By:\n"
+        for i, x in enumerate(sorted(variable.updated_by, key=lambda x: x.name)):
+            out += "{}. [[{}]]".format(i + 1, x.name)
+            out += "\n"
+        out += "\n"
+
         with open(
             "{}/State Variables/{}.md".format(
                 path, "{}-{}".format(state.name, variable.name)

{math_spec_mapping-0.3.15 → math_spec_mapping-0.3.17}/src/math_spec_mapping/__init__.py

@@ -30,6 +30,12 @@ from .Reports import (
     write_parameter_table_markdown,
 )
 from .schema import schema
-from .Convenience import remove_dummy_repo_components, write_scaffold_to_github_issues
+from .Convenience import (
+    remove_dummy_repo_components,
+    write_scaffold_to_github_issues,
+    find_open_issues,
+    create_priority_label_matrix,
+    create_milestone_label_matrix,
+)
 
 # from .Convenience import write_top_level_json_description

{math_spec_mapping-0.3.15 → math_spec_mapping-0.3.17/src/math_spec_mapping.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: math-spec-mapping
-Version: 0.3.15
+Version: 0.3.17
 Summary: A library for easy mapping of mathematical specifications.
 Author-email: Sean McOwen <Sean@Block.Science>
 Classifier: Programming Language :: Python :: 3

math_spec_mapping-0.3.15/src/math_spec_mapping/Convenience/__init__.py

@@ -1,3 +0,0 @@
-# from .documentation import write_top_level_json_description
-from .starter import remove_dummy_repo_components
-from .github import write_scaffold_to_github_issues

math_spec_mapping-0.3.15/src/math_spec_mapping/Convenience/github.py

@@ -1,34 +0,0 @@
-import os
-import requests
-
-
-def write_scaffold_to_github_issues(
-    scaffolder_folder, repo_owner, repository_name, access_token
-):
-    folders = [
-        x
-        for x in os.listdir(scaffolder_folder)
-        if os.path.isdir(scaffolder_folder + "/" + x)
-    ]
-    headers = {
-        "Accept": "application/vnd.github+json",
-        "X-GitHub-Api-Version": "2022-11-28",
-        "Authorization": "Bearer {}".format(access_token),
-    }
-    for folder in folders:
-        issue_name = "Write {} from MSML Scaffold".format(folder)
-        checklist = [
-            x[:-3]
-            for x in os.listdir(scaffolder_folder + "/" + folder)
-            if x.endswith(".md")
-        ]
-        checklist = ["- [ ] " + x for x in checklist]
-        checklist = "\n".join(checklist)
-
-        requests.post(
-            "https://api.github.com/repos/{}/{}/issues".format(
-                repo_owner, repository_name
-            ),
-            headers=headers,
-            json={"title": issue_name, "body": checklist},
-        )