adding H5MD-format writer

.travis.yml

@@ -38,6 +38,7 @@ env:
     - INSTALL_HOLE="true"
     - CYTHON_TRACE_NOGIL=1
     - MPLBACKEND=agg
+    - MAMBA=true
 
   matrix:
     # Run a coverage test for most versions
@@ -95,6 +96,29 @@ matrix:
            INSTALL_HOLE="false"
            CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
 
+    - os: linux
+      language: python
+      arch: arm64-graviton2
+      python:
+        - "3.7"
+      dist: focal
+      virt: vm
+      group: edge
+      before_install:
+        - python -m pip install cython numpy scipy
+        - python -m pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm
+      install:
+        - cd package
+        - python setup.py install
+        - cd ../testsuite
+        - python setup.py install
+        - cd ..
+      script:
+        - cd testsuite
+        - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 -rsx --cov=MDAnalysis
+      after_success:
+        - echo "Override this stage for ARM64"
+
   allow_failures:
     - env: NUMPY_VERSION=dev EVENT_TYPE="cron"
 

LICENSE

@@ -582,3 +582,45 @@ are distributed under the same license as the 'Atom' logo.
 
 ==========================================================================
 
+pyh5md is released under the following 'BSD 3-clause' licence:
+
+-----------------------------------------------------------------------------
+pyh5md
+
+    Author of Original Implementation:     
+                  Pierre de Buyl
+                  Institute for Theoretical Physics
+                  KU Leuven University
+                  Celestijnenlaan 200d - box 2415
+                  3001 Leuven
+
+                  pierre.debuyl@kuleuven.be
+
+    Copyright (c) 2012-2017, Pierre de Buyl and contributors
+    All rights reserved.
+
+    Redistribution and use in source and binary forms, with or without modification, are permitted 
+    provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright notice, this list of 
+      conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright notice, this list 
+      of conditions and the following disclaimer in the documentation and/or other materials 
+      provided with the distribution.
+    * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to 
+      endorse or promote products derived from this software without specific prior written 
+      permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+    PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+    HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+==========================================================================

README.rst

@@ -58,7 +58,7 @@ of MDAnalysis.
 
 **Developers** may also want to refer to the `MDAnalysis API docs`_.
 
-A growing number of **tutorials_** are available that explain how to
+A growing number of `tutorials`_ are available that explain how to
 conduct RMSD calculations, structural alignment, distance and contact
 analysis, and many more.
 

azure-pipelines.yml

@@ -54,7 +54,7 @@ jobs:
       pytest-xdist
       scikit-learn
       scipy
-      h5py
+      h5py==2.10.0
       tqdm
     displayName: 'Install dependencies'
   # TODO: recent rdkit is not on PyPI

maintainer/deploy_docs_via_travis.sh

@@ -53,17 +53,26 @@ git remote add upstream "https://${GH_TOKEN}@${GH_REPOSITORY}"
 git fetch --depth 50 upstream ${GH_DOC_BRANCH} gh-pages
 git reset upstream/gh-pages
 
-# for dev, latest, home redirects
-mkdir dev latest
+# === REDIRECTS AND COPIES ====
+# home (index.html) redirects to stable/
+# latest (latest/index.html) redirects to most recent release
+# dev/ is a copy of the dev docs with the highest number (so 2.0.0-dev instead of 1.0.1-dev)
+# stable/ is a copy of the release docs with the highest number
+mkdir latest
 export URL="https://docs.mdanalysis.org"
 python ${MAINTAIN_DIR}/update_json_stubs_sitemap.py
 touch .
 touch .nojekyll
 
 git add -A ${VERSION}/
 git add .nojekyll versions.json
-git add index.html dev latest
-git add *.xml
+git add index.html latest
+
+for dirname in dev stable documentation_pages ; do
+    if [ -d $dirname ]; then git add $dirname; fi
+done
+
+git add *.xml *.html
 
 # check for anything to commit
 # https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes

maintainer/update_json_stubs_sitemap.py

@@ -13,6 +13,10 @@
 import os
 import shutil
 import xml.etree.ElementTree as ET
+import errno
+import glob
+import textwrap
+import shutil
 
 try:
     from urllib.request import Request, urlopen
@@ -22,6 +26,16 @@
 URL = os.environ['URL']
 VERSION = os.environ['VERSION']
 
+if "http" not in URL:
+    raise ValueError("URL should have the transfer protocol (HTTP/S). "
+                     f"Given: $URL={URL}")
+
+try:
+    int(VERSION[0])
+except ValueError:
+    raise ValueError("$VERSION should start with a number. "
+                     f"Given: $VERSION={VERSION}") from None
+
 
 def get_web_file(filename, callback, default):
     url = os.path.join(URL, filename)
@@ -40,14 +54,30 @@ def get_web_file(filename, callback, default):
         return callback(data)
 
 
+def write_redirect(file, version='', outfile=None):
+    if outfile is None:
+        outfile = file
+    url = os.path.join(URL, version, file)
+    REDIRECT = textwrap.dedent(f"""
+    <!DOCTYPE html>
+    <meta charset="utf-8">
+    <title>Redirecting to {url}</title>
+    <meta http-equiv="refresh" content="0; URL={url}">
+    <link rel="canonical" href="{url}">
+    """)
+    with open(outfile, 'w') as f:
+        f.write(REDIRECT)
+    print(f"Wrote redirect from {url} to {outfile}")
+
+
 # ========= WRITE JSON =========
 # Update $root/versions.json with links to the right version
 versions = get_web_file('versions.json', json.loads, [])
 existing = [item['version'] for item in versions]
 already_exists = VERSION in existing
+latest = 'dev' not in VERSION
 
 if not already_exists:
-    latest = 'dev' not in VERSION
     if latest:
         for ver in versions:
             ver['latest'] = False
@@ -59,52 +89,112 @@ def get_web_file(filename, callback, default):
         'latest': latest
     })
 
-with open("versions.json", 'w') as f:
-    json.dump(versions, f, indent=2)
-
-# ========= WRITE HTML STUBS =========
-# Add HTML files to redirect:
-# index.html -> latest release
-# latest/index.html -> latest release
-# dev/index.html -> dev docs
-
-REDIRECT = """
-<!DOCTYPE html>
-<meta charset="utf-8">
-<title>Redirecting to {url}</title>
-<meta http-equiv="refresh" content="0; URL={url}">
-<link rel="canonical" href="{url}">
-"""
-
 for ver in versions[::-1]:
     if ver['latest']:
-        latest_url = ver['url']
+        latest_version = ver['version']
+        break
 else:
     try:
-        latest_url = versions[-1]['url']
+        latest_version = versions[-1]['version']
     except IndexError:
-        latest_url = None
+        latest_version = None
 
 for ver in versions[::-1]:
-    if 'dev' in ver['version']:
-        dev_url = ver['url']
+    if '-dev' in ver['version']:
+        dev_version = ver['version']
         break
 else:
     try:
-        dev_url = versions[-1]['url']
+        dev_version = versions[-1]['version']
     except IndexError:
-        dev_url = None
+        dev_version = None
 
-if latest_url:
-    with open('index.html', 'w') as f:
-        f.write(REDIRECT.format(url=latest_url))
+versions.sort(key=lambda x: x["version"])
 
-    with open('latest/index.html', 'w') as f:
-        f.write(REDIRECT.format(url=latest_url))
+# ========= WRITE HTML STUBS AND COPY DOCS =========
+# Add HTML files to redirect:
+# index.html -> stable/ docs
+# latest/index.html -> latest release (not dev docs)
+# stable/ : a copy of the release docs with the highest number (2.0.0 instead of 1.0.0)
+# dev/ : a copy of the develop docs with the highest number (2.0.0-dev instead of 1.0.1-dev)
+# sitemap.xml files are updated by replacing URL strings
+
+
+def redirect_sitemap(old_version, new_version):
+    """Replace paths in copied sitemap.xml with new directory path
+
+    Sitemaps can only contain URLs 'within' that directory structure.
+    For more, see https://www.sitemaps.org/faq.html#faq_sitemap_location
+    """
+    file = f"{new_version}/sitemap.xml"
+    old = f"{URL}/{old_version}/"
+    new = f"{URL}/{new_version}/"
+    try:
+        with open(file, "r") as f:
+            contents = f.read()
+    except OSError:
+        raise ValueError(f"{file} not found")
+    redirected = contents.replace(old, new)
+    with open(file, "w") as f:
+        f.write(redirected)
+    print(f"Redirected URLs in {file} from {old} to {new}")
+
+
+def add_or_update_version(version):
+    """Add or update the version path to versions.json"""
+    for ver in versions:
+        if ver["version"] == version:
+            ver["url"] = os.path.join(URL, version)
+            break
+        else:
+            versions.append({
+                "version": version,
+                "display": version,
+                "url": os.path.join(URL, version),
+                "latest": False
+            })
+
+
+def copy_version(old_version, new_version):
+    """Copy docs from one directory to another with all bells and whistles"""
+    shutil.copytree(old_version, new_version)
+    print(f"Copied {old_version} to {new_version}")
+    redirect_sitemap(old_version, new_version)
+    add_or_update_version(new_version)
+
+
+# Copy stable/ docs and write redirects from root level docs
+if latest:
+    copy_version(VERSION, "stable")
+    html_files = glob.glob(f'stable/**/*.html', recursive=True)
+    for file in html_files:
+        # below should be true because we only globbed stable/* paths
+        assert file.startswith("stable/")
+        outfile = file[7:]  # strip "stable/"
+        dirname = os.path.dirname(outfile)
+        if dirname and not os.path.exists(dirname):
+            try:
+                os.makedirs(dirname)
+            except OSError as exc:
+                if exc.errno != errno.EEXIST:
+                    raise
+
+        write_redirect(file, '', outfile)
+
+# Separate just in case we update versions.json or muck around manually
+# with docs
+if latest_version:
+    write_redirect('index.html', "stable")
+    write_redirect('index.html', latest_version, 'latest/index.html')
+
+# Copy dev/ docs
+if dev_version and dev_version == VERSION:
+    copy_version(VERSION, "dev")
+
+# update versions.json online
+with open("versions.json", 'w') as f:
+    json.dump(versions, f, indent=2)
 
-if dev_url:
-    with open('dev/index.html', 'w') as f:
-        f.write(REDIRECT.format(url=dev_url))
 
 # ========= WRITE SUPER SITEMAP.XML =========
 # make one big sitemap.xml