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Adding a formatter/check like astyle/codecheck #26

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24 changes: 23 additions & 1 deletion .github/workflows/main.yml
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Expand Up @@ -3,6 +3,29 @@ name: CI
on: [push, pull_request]

jobs:
check-code:
strategy:
fail-fast: false
matrix:
python-version: ["3.12"]
check: ["linting", "check-format"]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v5
with:
persist-credentials: false
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v6
with:
python-version: ${{ matrix.python-version }}
cache: 'pip'
cache-dependency-path: pyproject.toml
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install tox
- name: Check ${{ matrix.check }}
run: python -m tox -e ${{ matrix.check }}
#this is setting up a new "test workflow" following the one we use for the plumed-testcenter
setup-plumed:
runs-on: ubuntu-latest
Expand Down Expand Up @@ -117,7 +140,6 @@ jobs:
python -m pip install tox
- name: Run tests
run: |
#as now we do not want to be insulted by ruff, so only tests:
python -m tox -e tests

- name: Upload Coverage to Codecov
Expand Down
126 changes: 77 additions & 49 deletions check_inputs/create_inputs.py
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@@ -1,85 +1,113 @@
from pygments.styles import get_style_by_name
from pygments.formatters import HtmlFormatter
import os
import json
import PlumedToHTML

# Output css file for codehighlighting
ofile = open("codehilite.css", "w+")
ofile.write( HtmlFormatter(cssclass="codehilite", style='colorful').get_style_defs() )
ofile.write(HtmlFormatter(cssclass="codehilite", style="colorful").get_style_defs())
ofile.close()

print("<html>")
print('<meta charset="utf-8">')
print('<link rel="stylesheet" type="text/css" href="./codehilite.css">')
print('<meta name="viewport" content="width=device-width">')
print('<title>Example tutorial</title>')
print("<title>Example tutorial</title>")
print('<meta name="description" content="PLUMED website"/>')
print('<meta name="viewport" content="width=device-width, initial-scale=1">')
print('<meta name="theme-color" content="#157878">')
print('<link href=\'https://fonts.googleapis.com/css?family=Open+Sans:400,700\' rel=\'stylesheet\' type=\'text/css\'>')
print('<link rel="stylesheet" href="https://www.plumed.org//assets/css/style.css?v=9dd2bd3d9ee4823fb5d3485bda969afbaa1ba8d4">')
print('<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">')
print('<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/datatables.min.css"/>')
print('<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/jq-3.3.1/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/datatables.min.css"/>')
print('<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>')
print('<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>')
print('<script type="text/javascript" src="https://cdn.datatables.net/v/dt/jq-3.3.1/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/datatables.min.js"></script>')
print(
"<link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>"
)
print(
'<link rel="stylesheet" href="https://www.plumed.org//assets/css/style.css?v=9dd2bd3d9ee4823fb5d3485bda969afbaa1ba8d4">'
)
print(
'<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">'
)
print(
'<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/datatables.min.css"/>'
)
print(
'<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/jq-3.3.1/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/datatables.min.css"/>'
)
print(
'<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>'
)
print(
'<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>'
)
print(
'<script type="text/javascript" src="https://cdn.datatables.net/v/dt/jq-3.3.1/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/datatables.min.js"></script>'
)
print('<script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>')
print('<script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>')
print('</head>')
print('<body>')
print("</head>")
print("<body>")
print('<section class="page-header">')
print('<a href="https://github.com/plumed/plumed2"><img style="position:absolute; top:10px; right:100px; width:50px" src="https://www.plumed.org//Octocat.png" title="Get development version"></a>')
print('<a href="https://github.com/plumed/plumed2/releases/download/v2.8.0/plumed-2.8.0.tgz"><img style="position:absolute; top:10px; right:40px; width:40px" src="https://www.plumed.org//arrow.png" title="Get latest release"></a>')
print('<a class="site-title" href="http://www.plumed.org"><img width="220" src="pigeon-teacher.png"></a>')
print(
'<a href="https://github.com/plumed/plumed2"><img style="position:absolute; top:10px; right:100px; width:50px" src="https://www.plumed.org//Octocat.png" title="Get development version"></a>'
)
print(
'<a href="https://github.com/plumed/plumed2/releases/download/v2.8.0/plumed-2.8.0.tgz"><img style="position:absolute; top:10px; right:40px; width:40px" src="https://www.plumed.org//arrow.png" title="Get latest release"></a>'
)
print(
'<a class="site-title" href="http://www.plumed.org"><img width="220" src="pigeon-teacher.png"></a>'
)
print('<h1 class="project-name">PLUMED</h1>')
print('<h2 class="project-tagline">The community-developed PLUgin for MolEcular Dynamics</h2>')
print('</section>')
print(
'<h2 class="project-tagline">The community-developed PLUgin for MolEcular Dynamics</h2>'
)
print("</section>")
print('<section class="main-content">', flush=True)
# Putting this here You can see render the page while it is being generated
print( PlumedToHTML.get_html_header() )
print(PlumedToHTML.get_html_header())
f = open("./tdata/tests.json")
tests = json.load(f)
f.close()

for item in tests["regtests"] :
actions = set({})
out = PlumedToHTML.test_and_get_html( item["input"], "plinp" + str(item["index"]), actions=actions )

print(f"<h3>Input number {item['index']}</h3>")
#this visualizes the "from-to" and it is more clear to eye-check what is going on
print("<pre>")
print(item["input"])
print("</pre>")
print( out )
for item in tests["regtests"]:
actions = set({})
out = PlumedToHTML.test_and_get_html(
item["input"], "plinp" + str(item["index"]), actions=actions
)

print(f"<h3>Input number {item['index']}</h3>")
# this visualizes the "from-to" and it is more clear to eye-check what is going on
print("<pre>")
print(item["input"])
print("</pre>")
print(out)

f = open("./tdata/cltooltests.json")
tests = json.load(f)
f.close()

for item in tests["regtests"] :
out = PlumedToHTML.get_cltoolarg_html( item["input"], "clinp" + str(item["index"]), ("plumed",) )
#this visualizes the "from-to" and it is more clear to eye-check what is going on
print(f"<h3>CL tool input number {item['index']}</h3>")
print("<pre>")
print(item["input"])
print("</pre>")
print( out )
for item in tests["regtests"]:
out = PlumedToHTML.get_cltoolarg_html(
item["input"], "clinp" + str(item["index"]), ("plumed",)
)
# this visualizes the "from-to" and it is more clear to eye-check what is going on
print(f"<h3>CL tool input number {item['index']}</h3>")
print("<pre>")
print(item["input"])
print("</pre>")
print(out)

f = open("./tdata/clfiletests.json")
tests = json.load(f)
f.close()

for item in tests["regtests"] :
out = PlumedToHTML.get_cltoolfile_html( item["input"], "clinp" + str(item["index"]), ("plumed",) )
#this visualizes the "from-to" and it is more clear to eye-check what is going on
print(f"<h3>CL file input number {item['index']}</h3>")
print("<pre>")
print(item["input"])
print("</pre>")
print( out )
for item in tests["regtests"]:
out = PlumedToHTML.get_cltoolfile_html(
item["input"], "clinp" + str(item["index"]), ("plumed",)
)
# this visualizes the "from-to" and it is more clear to eye-check what is going on
print(f"<h3>CL file input number {item['index']}</h3>")
print("<pre>")
print(item["input"])
print("</pre>")
print(out)

print('</section>')
print('</body>')
print('</html>')
print("</section>")
print("</body>")
print("</html>")
41 changes: 22 additions & 19 deletions pyproject.toml
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Expand Up @@ -57,28 +57,31 @@ where = ["src"]
#we state which files we want to include per package
PlumedToHTML = ['assets/*.html']

[tool.ruff]
indent-width = 2

#this is not elegant, but having all the settings in a single file is cozier
[tool.tox]
legacy_tox_ini = """
[tox]
env_list =
tests
lint
requires = ["tox>=4.19"]
#enviroments run by simply calling "tox"
envlist=["format", "linting" , "tests"]

[testenv:tests]
deps = pytest
pytest-cov
commands = pytest --cov=PlumedToHTML --cov-report=term-missing
[tool.tox.env_run_base]
deps = ["pytest", "pytest-cov"]
commands = [[ "pytest", "tests", "--cov=PlumedToHTML", "--cov-report=term-missing"]]

[pytest]
testpaths =
tests
[tool.tox.env.linting]
skip_install = true
deps = ["ruff==0.9.6"]
commands = [["ruff", "check", "src/PlumedToHTML", "tests"]]

[testenv:lint]
[tool.tox.env.format]
skip_install = true
deps =
ruff==0.9.6
commands =
ruff check src/PlumedToHTML
ruff format src/PlumedToHTML --check
"""
deps = ["ruff==0.9.6"]
commands = [["ruff", "format", "src/PlumedToHTML", "tests"]]

[tool.tox.env.check-format]
skip_install = true
deps = ["ruff==0.9.6"]
commands = [["ruff", "format", "--check", "src/PlumedToHTML", "tests"]]

43 changes: 22 additions & 21 deletions src/PlumedToHTML/PlumedCLFileLexer.py
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@@ -1,24 +1,25 @@
from pygments.lexer import RegexLexer, bygroups, include
from pygments.token import Text, Keyword, Name, String, Comment
from pygments.lexer import RegexLexer, bygroups
from pygments.token import Text, Keyword, Name, Comment


class PlumedCLFileLexer(RegexLexer):
name = 'plumedclfile'
aliases = ['plumedclfile']
filenames = ['*.plmd']
name = "plumedclfile"
aliases = ["plumedclfile"]
filenames = ["*.plmd"]

tokens = {
'root': [
# Find the start of a shortcut with a nested default
(r'#NODEFAULT plumed\n',Comment.Special),
# Find the start of a default section
(r'#DEFAULT plumed\n',Comment.Special),
# Find the end of a default section
(r'#ENDDEFAULT plumed\n',Comment.Special),
# The name of the tool that this is an input file for
(r'(#TOOL=\s*)(\S+\b)',bygroups( Comment, Keyword )),
# The lines of instruction for the file
(r'(\S+\b)(\s+)(.+$)',bygroups(Name.Attribute, Text, Text)),
# Find any left over white space
(r'\s+',Text)
]
}
tokens = {
"root": [
# Find the start of a shortcut with a nested default
(r"#NODEFAULT plumed\n", Comment.Special),
# Find the start of a default section
(r"#DEFAULT plumed\n", Comment.Special),
# Find the end of a default section
(r"#ENDDEFAULT plumed\n", Comment.Special),
# The name of the tool that this is an input file for
(r"(#TOOL=\s*)(\S+\b)", bygroups(Comment, Keyword)),
# The lines of instruction for the file
(r"(\S+\b)(\s+)(.+$)", bygroups(Name.Attribute, Text, Text)),
# Find any left over white space
(r"\s+", Text),
]
}
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