feat: implement somesy fill command with Jinja templating (closes #42)

Materials-Data-Science-and-Informatics · Aug 17, 2023 · 5092b00 · 5092b00
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -82,9 +82,16 @@ repos:
     - repo: local
       hooks:
         # NOTE: copy from .pre-commit-hooks.yaml, for technical reasons
-        - id: somesy
-          name: somesy
+        - id: somesy-sync
+          name: Run somesy sync
           entry: somesy sync
           language: python
           files: '^\.somesy\.toml|pyproject\.toml$'
           pass_filenames: false
+
+        - id: somesy-fill
+          name: Update AUTHORS.md
+          entry: somesy fill -t docs/_template_authors.md -o AUTHORS.md
+          language: python
+          files: '^\.somesy\.toml|pyproject\.toml$'
+          pass_filenames: false
diff --git a/.pre-commit-hooks.yaml b/.pre-commit-hooks.yaml
@@ -1,7 +1,8 @@
 - id: somesy
   name: somesy
   description: Sync your metadata files with somesy
-  entry: somesy sync
+  entry: somesy
+  args: ["sync"]
   language: python
   files: '^somesy\.toml|\.somesy\.toml|pyproject\.toml|package\.json$'
   pass_filenames: false
diff --git a/.somesy.toml b/.somesy.toml
@@ -13,7 +13,7 @@ given-names = "Mustafa"
 email = "m.soylu@fz-juelich.de"
 orcid = "https://orcid.org/0000-0003-2637-0432"
 
-contribution = "The main developer, maintainer and tester."
+contribution = "Main developer, maintainer and tester."
 contribution_begin = "2023-03-01"
 contribution_types = ["maintenance", "code", "test", "review", "doc"]
 
@@ -26,7 +26,7 @@ given-names = "Anton"
 email = "a.pirogov@fz-juelich.de"
 orcid = "https://orcid.org/0000-0002-5077-7497"
 
-contribution = "Initial concepts, tool development and enhancement, documentation."
+contribution = "Concepts, tool development and enhancement, documentation."
 contribution_begin = "2023-03-01"
 contribution_types = ["ideas", "code", "test", "review", "doc"]
 

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -1,38 +1,42 @@
 # Authors and Contributors
 
-**Main authors** are persons whose contributions significantly shaped
-the state of the software at some point in time.
+**Authors** are people whose contributions significantly shaped
+the state of `somesy` at some point in time.
 
-**Additional contributors** are persons who are not main authors,
-but contributed non-trivially to this project,
-e.g. by providing smaller fixes and enhancements to the code and/or documentation.
+**Additional contributors** are people who contributed non-trivially to this project
+in different ways, e.g. by providing smaller fixes and enhancements to the code
+and/or documentation.
 
 Of course, this is just a rough overview and categorization.
 For a more complete overview of all contributors and contributions,
 please inspect the git history of this repository.
 
-## Main Authors
+## Authors
 
 - Mustafa Soylu (
   [E-Mail](mailto:m.soylu@fz-juelich.de),
   [ORCID](https://orcid.org/0000-0003-2637-0432)
-  ): original author
-
+  ): Main developer, maintainer and tester.
 - Anton Pirogov (
   [E-Mail](mailto:a.pirogov@fz-juelich.de),
   [ORCID](https://orcid.org/0000-0002-5077-7497)
-  ): documentation, review, and ideas
+  ): Concepts, tool development and enhancement, documentation.
 
-## Additional Contributors
 
-<!--
-- Name (E-mail, ORCID):
-Summary of contribution
--->
+## Additional Contributors
 
 - Jens Bröder (
   [E-Mail](mailto:j.broeder@fz-juelich.de),
   [ORCID](https://orcid.org/0000-0001-7939-226X)
-  ): ideas
-
-... maybe **[you](https://materials-data-science-and-informatics.github.io/somesy/main/contributing)**?
+  ): Discussions and suggestions concerning metadata standards and usability.
+- Volker Hofmann (
+  [E-Mail](mailto:v.hofmann@fz-juelich.de),
+  [ORCID](https://orcid.org/0000-0002-5149-603X)
+  ): Discussions and suggestions concerning tool scope and usability.
+- Stefan Sandfeld (
+  [E-Mail](mailto:s.sandfeld@fz-juelich.de),
+  [ORCID](https://orcid.org/0000-0001-9560-4728)
+  )
+
+
+... maybe **[you](https://materials-data-science-and-informatics.github.io/somesy/latest/contributing)**?
diff --git a/CITATION.cff b/CITATION.cff
@@ -15,10 +15,6 @@ authors:
   email: m.soylu@fz-juelich.de
   given-names: Mustafa
   family-names: Soylu
-- orcid: https://orcid.org/0000-0002-5077-7497
-  email: a.pirogov@fz-juelich.de
-  given-names: Anton
-  family-names: Pirogov
 - email: v.hofmann@fz-juelich.de
   orcid: https://orcid.org/0000-0002-5149-603X
   family-names: Hofmann
@@ -27,6 +23,10 @@ authors:
   orcid: https://orcid.org/0000-0001-9560-4728
   family-names: Sandfeld
   given-names: Stefan
+- email: a.pirogov@fz-juelich.de
+  orcid: https://orcid.org/0000-0002-5077-7497
+  family-names: Pirogov
+  given-names: Anton
 contact:
 - email: m.soylu@fz-juelich.de
   family-names: Soylu

diff --git a/codemeta.json b/codemeta.json
@@ -11,14 +11,20 @@
     "audience": [
         {
             "@type": "Audience",
-            "audienceType": "Developers"
+            "audienceType": "Science/Research"
         },
         {
             "@type": "Audience",
-            "audienceType": "Science/Research"
+            "audienceType": "Developers"
         }
     ],
     "author": [
+        {
+            "@id": "https://orcid.org/0000-0003-2637-0432",
+            "@type": "Person",
+            "familyName": "Soylu",
+            "givenName": "Mustafa"
+        },
         {
             "@id": "https://orcid.org/0000-0002-5149-603X",
             "@type": "Person",
@@ -31,12 +37,6 @@
             "familyName": "Sandfeld",
             "givenName": "Stefan"
         },
-        {
-            "@id": "https://orcid.org/0000-0003-2637-0432",
-            "@type": "Person",
-            "familyName": "Soylu",
-            "givenName": "Mustafa"
-        },
         {
             "@id": "https://orcid.org/0000-0002-5077-7497",
             "@type": "Person",
@@ -91,6 +91,13 @@
             "runtimePlatform": "Python 3",
             "version": "^4.11.0"
         },
+        {
+            "@type": "SoftwareApplication",
+            "identifier": "jinja2",
+            "name": "jinja2",
+            "runtimePlatform": "Python 3",
+            "version": "^3.1.2"
+        },
         {
             "@type": "SoftwareApplication",
             "identifier": "packaging",

diff --git a/docs/_template_authors.md b/docs/_template_authors.md
@@ -0,0 +1,35 @@
+# Authors and Contributors
+
+**Authors** are people whose contributions significantly shaped
+the state of `{{ project.name }}` at some point in time.
+
+**Additional contributors** are people who contributed non-trivially to this project
+in different ways, e.g. by providing smaller fixes and enhancements to the code
+and/or documentation.
+
+Of course, this is just a rough overview and categorization.
+For a more complete overview of all contributors and contributions,
+please inspect the git history of this repository.
+
+## Authors
+
+{% for p in project.authors() %}
+{%- set contr_desc = p.contribution or "" -%}
+- {{ p.full_name }} (
+  [E-Mail](mailto:{{ p.email }}),
+  [ORCID]({{ p.orcid }})
+  ){{ ": "+contr_desc if contr_desc else "" }}
+{% endfor %}
+
+## Additional Contributors
+
+{% for p in project.contributors() %}
+{%- set contr_desc = p.contribution or "" -%}
+- {{ p.full_name }} (
+  [E-Mail](mailto:{{ p.email }}),
+  [ORCID]({{ p.orcid }})
+  ){{ ": "+contr_desc if contr_desc else "" }}
+{% endfor %}
+
+... maybe **[you](https://materials-data-science-and-informatics.github.io/somesy/latest/contributing)**?
+
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -143,6 +143,9 @@ plugins:
       enabled: !ENV [OFFLINE, false]
   # to make multi-version docs work right
   - mike
+  - exclude:
+      glob:
+        - "_*.md"  # for internal purposes
 
 hooks:
   - docs/scripts/coverage_status.py

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -45,6 +45,7 @@ wrapt = "^1.15.0"
 packaging = "^23.1"
 rdflib = "^6.3.2"
 codemetapy = "^2.5.0"
+jinja2 = "^3.1.2"
 
 [tool.poetry.group.dev.dependencies]
 poethepoet = "^0.18.1"
@@ -76,6 +77,7 @@ mike = "^1.1.2"
 anybadge = "^1.14.0"
 interrogate = "^1.5.0"
 black = "^23.3.0"
+mkdocs-exclude = "^1.0.2"
 
 [tool.poetry.scripts]
 somesy = "somesy.main:app"
@@ -99,9 +101,10 @@ licensecheck = "licensecheck"  # run this when you add new deps
 pythonpath = ["src"]
 addopts = "--cov-report=term-missing:skip-covered"
 filterwarnings = [
-"ignore::DeprecationWarning:pkg_resources.*"
+"ignore::DeprecationWarning:pkg_resources.*",
+"ignore::DeprecationWarning:pyshacl.*",
 # Example:
-# "ignore::DeprecationWarning:importlib_metadata.*"
+# "ignore::DeprecationWarning:importlib_metadata.*",
 ]
 
 [tool.coverage.run]

diff --git a/src/somesy/cli/fill.py b/src/somesy/cli/fill.py
@@ -0,0 +1,74 @@
+"""Fill command of somesy."""
+import logging
+from pathlib import Path
+from sys import stdin
+
+import typer
+from jinja2 import Environment, FileSystemLoader, FunctionLoader, select_autoescape
+
+from somesy.core.core import discover_input
+
+from ..core.models import SomesyInput
+from .util import wrap_exceptions
+
+logger = logging.getLogger("somesy")
+app = typer.Typer()
+
+
+@app.callback(invoke_without_command=True)
+@wrap_exceptions
+def fill(
+    template_file: Path = typer.Option(
+        None,
+        "--template",
+        "-t",
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=False,
+        help="Path to a Jinja2 template for somesy to fill (default: stdin).",
+    ),
+    input_file: Path = typer.Option(
+        None,
+        "--input-file",
+        "-i",
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=True,
+        readable=True,
+        resolve_path=True,
+        help="Path of somesy input file (default: try to infer).",
+    ),
+    output_file: Path = typer.Option(
+        None,
+        "--output-file",
+        "-o",
+        exists=False,
+        file_okay=True,
+        dir_okay=False,
+        writable=True,
+        readable=False,
+        resolve_path=True,
+        help="Path for target file (default: stdout).",
+    ),
+):
+    """Fill a Jinja2 template with somesy project metadata (e.g. list authors in project docs)."""
+    somesy_input = SomesyInput.from_input_file(discover_input(input_file))
+    if template_file:
+        env = Environment(loader=FileSystemLoader("."), autoescape=select_autoescape())
+        template = env.get_template(str(template_file))
+    else:
+        env = Environment(
+            loader=FunctionLoader(lambda _: stdin.read()),
+            autoescape=select_autoescape(),
+        )
+        template = env.get_template("")
+    result = template.render(project=somesy_input.project)
+    if not output_file:
+        print(result)
+    else:
+        with open(output_file, "w") as f:
+            f.write(result)
diff --git a/src/somesy/cli/sync.py b/src/somesy/cli/sync.py
@@ -53,7 +53,7 @@ def sync(
     ),
     no_sync_package_json: bool = typer.Option(
         None,
-        "--sync-package-json",
+        "--no-sync-package-json",
         "-J",
         help="Do not sync package.json file (default: False)",
     ),