From 875bd8e5d4522acfd67a20bd982407ed88e9e96b Mon Sep 17 00:00:00 2001
From: Karim Ahmed <karim.ahmed@xfel.eu>
Date: Tue, 22 Feb 2022 16:57:34 +0100
Subject: [PATCH] FIX + Doc / Build_readthedocs_documentation
---
.readthedocs.yaml | 21 +++++++++
docs/requirements.txt | 1 +
docs/source/conf.py | 51 +++++++++-----------
notebooks/test/test-cli.ipynb | 23 +++++++--
setup.py | 82 ++++++++++++++++++---------------
src/xfel_calibrate/calibrate.py | 3 +-
src/xfel_calibrate/nb_args.py | 5 +-
7 files changed, 114 insertions(+), 72 deletions(-)
create mode 100644 .readthedocs.yaml
create mode 100644 docs/requirements.txt
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 000000000..a021856d4
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+ configuration: docs/source/conf.py
+ fail_on_warning: false
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+ version: 3.8
+ install:
+ - requirements: docs/requirements.txt
+ - method: pip
+ path: .
+ extra_requirements:
+ - docs
diff --git a/docs/requirements.txt b/docs/requirements.txt
new file mode 100644
index 000000000..8c3d97346
--- /dev/null
+++ b/docs/requirements.txt
@@ -0,0 +1 @@
+iCalibrationDB @ git+https://xcalgitlab:${GITHUB_TOKEN}@git.xfel.eu/gitlab/detectors/cal_db_interactive.git@2.0.9
\ No newline at end of file
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 693a632c4..5112b0010 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -13,6 +13,8 @@
# All configuration values have a default; values that are commented out
# serve to show the default.
+import glob
+
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -20,6 +22,23 @@
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
+import os
+import shutil
+import sys
+import textwrap
+from datetime import datetime
+from subprocess import Popen, check_output
+from textwrap import dedent, indent
+from uuid import uuid4
+
+import nbformat
+import tabulate
+from dateutil.parser import parse
+from lxml import etree
+from nbconvert import RSTExporter
+
+# generate the list of available notebooks
+from xfel_calibrate import notebooks
# -- General configuration ------------------------------------------------
@@ -39,11 +58,6 @@ extensions = [
'sphinx.ext.viewcode',
]
-import glob
-import os
-import sys
-from subprocess import Popen
-
sys.path.append(os.path.abspath("../pycalibration/"))
p = Popen(["./makeAllDocs.sh"])
p.communicate()
@@ -374,18 +388,7 @@ except:
check_call(["wget", pandoc_url])
check_call(["dpkg", "-i", pandoc_pack])
-import os
-from subprocess import check_output
-from textwrap import dedent, indent
-
-import nbformat
-from nbconvert import RSTExporter
-
-# generate the list of available notebooks
-from xfel_calibrate import notebooks
-
rst_exporter = RSTExporter()
-
with open("available_notebooks.rst", "w") as f:
f.write(dedent("""
.. _available_notebooks:
@@ -407,7 +410,8 @@ with open("available_notebooks.rst", "w") as f:
for caltype in sorted(values.keys()):
data = values[caltype]
-
+ if data.get("notebook", None) is None:
+ continue
nbpath = os.path.abspath("{}/../../../{}".format(__file__, data["notebook"]))
with open(nbpath, "r") as nf:
nb = nbformat.read(nf, as_version=4)
@@ -440,16 +444,7 @@ with open("available_notebooks.rst", "w") as f:
f.write("\n\n")
# add test results
-test_artefact_dir = os.path.realpath("../../tests/artefacts")
-
-import shutil
-import textwrap
-from datetime import datetime
-from uuid import uuid4
-
-import tabulate
-from dateutil.parser import parse
-from lxml import etree
+test_artefact_dir = os.path.realpath("../../tests/legacy/artefacts")
def xml_to_rst_report(xml, git_tag, reports=[]):
@@ -575,7 +570,6 @@ Contents:
"""
if not os.path.exists("./test_rsts"):
os.makedirs("./test_rsts")
-
with open("test_results.rst", "w") as f:
f.write(header)
for commit, modtime in sorted_dir(test_artefact_dir):
@@ -610,5 +604,6 @@ with open("test_results.rst", "w") as f:
fr.write(rst)
f.write(" test_rsts/{}\n".format(commit))
+
def setup(app):
app.add_stylesheet('css/test_decorators.css')
diff --git a/notebooks/test/test-cli.ipynb b/notebooks/test/test-cli.ipynb
index 4367676b1..daacfb223 100644
--- a/notebooks/test/test-cli.ipynb
+++ b/notebooks/test/test-cli.ipynb
@@ -75,9 +75,24 @@
}
],
"metadata": {
- "language_info": {},
- "orig_nbformat": 3
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.12"
+ }
},
"nbformat": 4,
- "nbformat_minor": 0
-}
\ No newline at end of file
+ "nbformat_minor": 4
+}
diff --git a/setup.py b/setup.py
index c0ed5ebc2..926dde6e6 100644
--- a/setup.py
+++ b/setup.py
@@ -1,11 +1,12 @@
+import sys
from distutils.command.build import build
from subprocess import check_output
import numpy
from Cython.Build import cythonize
from Cython.Distutils import build_ext
-from setuptools.extension import Extension
from setuptools import find_packages, setup
+from setuptools.extension import Extension
from src.xfel_calibrate.notebooks import notebooks
@@ -40,43 +41,10 @@ for ctypes in notebooks.values():
data_files = list(filter(None, data_files)) # Get rid of `None` entries
-setup(
- name="European XFEL Offline Calibration",
- version="1.0",
- author="Steffen Hauf",
- author_email="steffen.hauf@xfel.eu",
- maintainer="EuXFEL Calibration Team",
- url="",
- description="",
- long_description="",
- long_description_content_type="text/markdown",
- # TODO: find licence, assuming this will be open sourced eventually
- license="(c) European XFEL GmbH 2018",
- packages=find_packages("src"),
- package_dir={"": "src"},
- package_data={
- "xfel_calibrate": [
- "bin/*.sh",
- "titlepage.tmpl",
- "xfel.pdf",
- ]
- + data_files
- },
- entry_points={
- "console_scripts": [
- "xfel-calibrate = xfel_calibrate.calibrate:run",
- ],
- },
- cmdclass={
- "build": PreInstallCommand,
- "build_ext": build_ext,
- },
- ext_modules=cythonize(ext_modules, language_level=3),
- install_requires=[
- "iCalibrationDB @ git+ssh://git@git.xfel.eu:10022/detectors/cal_db_interactive.git@2.0.9", # noqa
- "XFELDetectorAnalysis @ git+ssh://git@git.xfel.eu:10022/karaboDevices/pyDetLib.git@2.7.0", # noqa
+install_requires = [
"Cython==0.29.21",
"Jinja2==2.11.2",
+ "markupsafe==2.0.1",
"astcheck==0.2.5",
"astsearch==0.2.0",
"cfelpyutils==1.0.1",
@@ -121,7 +89,47 @@ setup(
"sphinx==1.8.5",
"tabulate==0.8.6",
"traitlets==4.3.3",
- ],
+]
+
+if "readthedocs.org" not in sys.executable:
+ install_requires += [
+ "iCalibrationDB @ git+ssh://git@git.xfel.eu:10022/detectors/cal_db_interactive.git@2.0.9", # noqa
+ "XFELDetectorAnalysis @ git+ssh://git@git.xfel.eu:10022/karaboDevices/pyDetLib.git@2.7.0", # noqa
+ ]
+
+setup(
+ name="European XFEL Offline Calibration",
+ version="1.0",
+ author="Steffen Hauf",
+ author_email="steffen.hauf@xfel.eu",
+ maintainer="EuXFEL Calibration Team",
+ url="",
+ description="",
+ long_description="",
+ long_description_content_type="text/markdown",
+ # TODO: find licence, assuming this will be open sourced eventually
+ license="(c) European XFEL GmbH 2018",
+ packages=find_packages("src"),
+ package_dir={"": "src"},
+ package_data={
+ "xfel_calibrate": [
+ "bin/*.sh",
+ "titlepage.tmpl",
+ "xfel.pdf",
+ ]
+ + data_files
+ },
+ entry_points={
+ "console_scripts": [
+ "xfel-calibrate = xfel_calibrate.calibrate:run",
+ ],
+ },
+ cmdclass={
+ "build": PreInstallCommand,
+ "build_ext": build_ext,
+ },
+ ext_modules=cythonize(ext_modules, language_level=3),
+ install_requires=install_requires,
extras_require={
"docs": [
"nbsphinx",
diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index 19f46fdef..b0cc47655 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -558,7 +558,8 @@ def make_par_table(parms, run_tmp_path: str):
def run(argv=None):
""" Run a calibration task with parser arguments """
# Ensure files are opened as UTF-8 by default, regardless of environment.
- locale.setlocale(locale.LC_CTYPE, ('en_US', 'UTF-8'))
+ if "readthedocs.org" not in sys.executable:
+ locale.setlocale(locale.LC_CTYPE, ('en_US', 'UTF-8'))
if argv is None:
argv = sys.argv
diff --git a/src/xfel_calibrate/nb_args.py b/src/xfel_calibrate/nb_args.py
index bdf4a7d5e..e768d9f63 100644
--- a/src/xfel_calibrate/nb_args.py
+++ b/src/xfel_calibrate/nb_args.py
@@ -317,7 +317,8 @@ def extend_params(nb, extend_func_name, argv):
# Make a temporary parser that won't exit if it sees -h or --help
pre_parser = make_initial_parser(add_help=False)
- add_args_from_nb(nb, pre_parser, no_required=True)
+ params = extract_parameters(nb, lang='python')
+ add_args_from_nb(params, pre_parser, no_required=True)
known, _ = pre_parser.parse_known_args(argv[1:])
args = deconsolize_args(vars(known))
@@ -328,7 +329,7 @@ def extend_params(nb, extend_func_name, argv):
extension = f(*[args[p] for p in sig.parameters])
fcc = first_code_cell(nb)
- fcc["source"] += "\n" + extension
+ fcc["source"] += "\n" + extension if extension else "\n"
@dataclass
--
GitLab