Merge pull request nschloe#212 from nschloe/pypi-markdown

Pypi markdown, gmsh fixes

.circleci/config.yml

@@ -17,11 +17,6 @@ jobs:
       - run: pip3 install .[exodus,hdf5]
       # Make sure to get numpy 1.13.0
       - run: pip3 install -U numpy
-      # make sure that rst converts correctly
-      - run: apt install -y pandoc
-      - run: pip3 install docutils pygments
-      - run: make README.rst
-      - run: python3 setup.py check -r -s
       # The actual test
       - run: pylint setup.py meshio/ test/*.py tools/meshio-convert
       - run: cd test/ && pytest --cov meshio

Makefile

@@ -3,26 +3,25 @@ VERSION=$(shell python3 -c "import meshio; print(meshio.__version__)")
 default:
 	@echo "\"make publish\"?"
 
-README.rst: README.md
-	cat README.md | sed -e 's_<img src="\([^"]*\)" width="\([^"]*\)">_![](\1){width="\2"}_g' -e 's_<p[^>]*>__g' -e 's_</p>__g' > /tmp/README.md
-	pandoc /tmp/README.md -o README.rst
-	python3 setup.py check -r -s || exit 1
+tag:
+	@if [ "$(shell git rev-parse --abbrev-ref HEAD)" != "master" ]; then exit 1; fi
+	@echo "Tagging v$(VERSION)..."
+	git tag v$(VERSION)
+	git push --tags
 
-upload: setup.py README.rst
+upload: setup.py
 	# Make sure we're on the master branch
 	@if [ "$(shell git rev-parse --abbrev-ref HEAD)" != "master" ]; then exit 1; fi
 	rm -f dist/*
+	python3 setup.py sdist
 	python3 setup.py bdist_wheel --universal
 	gpg --detach-sign -a dist/*
-	twine upload dist/*
-
-tag:
-	@if [ "$(shell git rev-parse --abbrev-ref HEAD)" != "master" ]; then exit 1; fi
-	@echo "Tagging v$(VERSION)..."
-	git tag v$(VERSION)
-	git push --tags
+	# https://dustingram.com/articles/2018/03/16/markdown-descriptions-on-pypi
+	twine upload dist/*.tar.gz
+	twine upload dist/*.whl
 
 publish: tag upload
 
 clean:
-	rm -f README.rst
+	@find . | grep -E "(__pycache__|\.pyc|\.pyo$\)" | xargs rm -rf
+	@rm -rf *.egg-info/ build/ dist/

README.md

@@ -3,9 +3,9 @@
 [![CircleCI](https://img.shields.io/circleci/project/github/nschloe/meshio/master.svg)](https://circleci.com/gh/nschloe/meshio)
 [![codecov](https://img.shields.io/codecov/c/github/nschloe/meshio.svg)](https://codecov.io/gh/nschloe/meshio)
 [![Codacy grade](https://img.shields.io/codacy/grade/dc23fe7f7d4540b0a405110b3ae97dc6.svg)](https://app.codacy.com/app/nschloe/meshio/dashboard)
-[![PyPi Version](https://img.shields.io/pypi/v/meshio.svg)](https://pypi.python.org/pypi/meshio)
+[![PyPi Version](https://img.shields.io/pypi/v/meshio.svg)](https://pypi.org/project/meshio)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1173115.svg)](https://doi.org/10.5281/zenodo.1173115)
-[![GitHub stars](https://img.shields.io/github/stars/nschloe/meshio.svg?logo=github&style=social&label=Stars)](https://github.com/nschloe/meshio)
+[![GitHub stars](https://img.shields.io/github/stars/nschloe/meshio.svg?logo=github&label=Stars)](https://github.com/nschloe/meshio)
 
 <p align="center">
   <img src="https://nschloe.github.io/meshio/meshio_logo.png" width="20%">
@@ -68,7 +68,7 @@ For both input and output, you can optionally specify the exact `file_format`
 ### Installation
 
 meshio is [available from the Python Package
-Index](https://pypi.python.org/pypi/meshio/), so simply type
+Index](https://pypi.org/project/meshio/), so simply type
 ```
 pip install -U meshio
 ```

meshio/__about__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-__version__ = '1.11.9'
+__version__ = '1.11.10'
 __author__ = u'Nico Schlömer'
 __author_email__ = '[email protected]'
 __copyright__ = \

meshio/dolfin_io.py

@@ -241,16 +241,12 @@ def write(filename,
         assert 'triangle' in cells
         cell_type = 'triangle'
 
-    print('a')
     _write_mesh(filename, points, cell_type, cells)
 
-    print('b')
-
     if cell_type in cell_data:
         for key, data in cell_data[cell_type].items():
             cell_data_filename = \
                 '{}_{}.xml'.format(os.path.splitext(filename)[0], key)
             dim = 2 if all(points[:, 2] == 0) else 3
             _write_cell_data(cell_data_filename, dim, numpy.array(data))
-    print('c')
     return

meshio/gmsh_io.py

@@ -273,7 +273,7 @@ def _read_data(f, tag, data_dict, int_size, data_size, is_ascii):
     # Read string tags
     num_string_tags = int(f.readline().decode('utf-8'))
     string_tags = [
-        f.readline().decode('utf-8').strip()
+        f.readline().decode('utf-8').strip().replace('"', '')
         for _ in range(num_string_tags)
         ]
     # The real tags typically only contain one value, the time.
@@ -468,6 +468,7 @@ def _write_elements(fh, cells, tag_data, write_binary):
                 )[:, numpy.newaxis]
             a += 1 + consecutive_index
             array = numpy.hstack([a, fcd, node_idcs + 1])
+            assert array.dtype == numpy.int32
             fh.write(array.tostring())
         else:
             form = '{} ' + str(_meshio_to_gmsh_type[cell_type]) \
@@ -498,7 +499,7 @@ def _write_data(fh, tag, name, data, write_binary):
     # > the second as the name of the interpolation scheme. The interpolation
     # > scheme is provided in the $InterpolationScheme section (see below).
     fh.write('{}\n'.format(1).encode('utf-8'))
-    fh.write('{}\n'.format(name).encode('utf-8'))
+    fh.write('"{}"\n'.format(name).encode('utf-8'))
     fh.write('{}\n'.format(1).encode('utf-8'))
     fh.write('{}\n'.format(0.0).encode('utf-8'))
     # three integer tags:
@@ -583,7 +584,7 @@ def write(filename,
             other_data[cell_type] = {}
             for key, data in a.items():
                 if key in ['gmsh:physical', 'gmsh:geometrical']:
-                    tag_data[cell_type][key] = data
+                    tag_data[cell_type][key] = data.astype(numpy.int32)
                 else:
                     other_data[cell_type][key] = data
 

meshio/helpers.py

@@ -96,6 +96,9 @@ def read(filename, file_format=None):
     if not file_format:
         # deduce file format from extension
         extension = '.' + os.path.basename(filename).split(os.extsep, 1)[-1]
+        assert extension in _extension_to_filetype, \
+            'Could not deduce file format from extension \'{}\'.' \
+            .format(extension)
         file_format = _extension_to_filetype[extension]
 
     format_to_reader = {
@@ -128,6 +131,9 @@ def read(filename, file_format=None):
         'exodus': exodus_io,
         }
 
+    assert file_format in format_to_reader, \
+        'Unknown file format \'{}\' of \'{}\'.'.format(file_format, filename)
+
     return format_to_reader[file_format].read(filename)
 
 
@@ -153,6 +159,9 @@ def write(filename,
     if not file_format:
         # deduce file format from extension
         extension = '.' + os.path.basename(filename).split(os.extsep, 1)[-1]
+        assert extension in _extension_to_filetype, \
+            'Could not deduce file format from extension \'{}\'.' \
+            .format(extension)
         file_format = _extension_to_filetype[extension]
 
     # check cells for sanity

setup.py

@@ -14,14 +14,7 @@
 
 
 def read(fname):
-    try:
-        content = codecs.open(
-            os.path.join(base_dir, fname),
-            encoding='utf-8'
-            ).read()
-    except IOError:
-        content = ''
-    return content
+    return codecs.open(os.path.join(base_dir, fname), encoding='utf-8').read()
 
 
 setup(
@@ -31,16 +24,20 @@ def read(fname):
     author_email=about['__author_email__'],
     packages=find_packages(),
     description='I/O for various mesh formats',
-    long_description=read('README.rst'),
+    long_description=read('README.md'),
+    long_description_content_type='text/markdown',
     url='https://github.com/nschloe/meshio',
-    download_url='https://pypi.python.org/pypi/meshio',
+    project_urls={
+        'Issues': 'https://github.com/nschloe/meshio/issues',
+        },
     license=about['__license__'],
     platforms='any',
     install_requires=[
         'numpy',
         'pipdate',
         ],
     extras_require={
+        'all': ['netCDF4', 'h5py'],
         'exodus': ['netCDF4'],
         'hdf5': ['h5py'],  # MED, MOAB, XDMF formats
         },