Unraveling complex biology with biological knowledge graphs. Content licensed under CC BY 4.0.

Charles Tapley Hoyt

PEP 735 introduced dependency groups in packaging metadata, which are complementary to optional dependencies in that they might not correspond to features in the package, but rather be something like development or release dependencies. I am slowly working towards updating my cookiecutter template cookiecutter-snekpack to use PEP 735. So far, uv and tox have released support - all that’s left is ReadTheDocs.

Dependency Groups and ReadTheDocs

I’m working through making a contribution to pandoc that adds first-class support for author role annotations using the Contribution Role Taxonomy (CRediT) and also outputs compliant Journal Publishing Tag Set (JATS) XML. This has lead me down a (losing) journey with learning the Haskell programming language, so I thought I would post a short note on a function I tried to understand.

Some Haskell I Tried to Write

Graphviz is software for graph visualization written in C. PyGraphviz provides a nice Python wrapper for it. The issue is that getting Python to know about the C headers changes every few months. I’ll try and keep this blog post updated every time there are some changes.

Building Graphviz when installing PyGraphviz

Several controlled vocabularies and ontologies that aren’t themselves OBO Foundry ontologies use unsanctioned OBO PURLs. This post is about how to use the Bioregistry to identify which resources are doing this and to give some insight into how we arrived in this situation. Background on the OBO Foundry   The OBO Foundry is a set of independent, interoperable biomedical ontologies that aspire to using shared development principles.

Resources masquerading as OBO Foundry ontologies

Today’s short post is about three SPARQL queries I wrote to get bibliometric information about journals and publishers out of Wikidata. Each of the following queries can be readily copy-pasted into the Wikidata Query Service and run in the browser.

Querying Journals and Publishers in Wikidata

I’ve just returned from the 17

 th

Annual International Biocuration Conference at the Indian Biological Data Centre (IBDC) in Faridabad, India.

Discussions and Follow-ups from Biocuration 2024

Using Pydantic for encoding data models and FastAPI for implementing APIs on top of them has become a staple for many Python programmers.

Semantic Pydantic

I finally got back into reading! Over winter break 2022, I started the Stormlight Archive then followed up in 2023 by reading the entirety of Brandon Sanderson’s

 Cosmere

, as well as a some other fantasy, science fiction, and literary fiction. Here’s the list.

Books I Read in 2023

Archival Resource Keys (ARKs) are flavor of persistent identifiers like DOIs, URNs, and Handles that have the benefit of being free, flexible with what metadata gets attached, and natively able to resolve to web pages. Name-to-Thing (N2T) implements a resolver for a variety of ARKs, so this blog post is about how that resolver can be re-implemented with the curies Python package. In a lot of ways, ARKs look and act like CURIEs.

Re-implementing the N2T ARK Resolver

This blog is normally about

 very serious science

, but I’m taking a break from that for the evening to advertize my band’s upcoming show on April 8

 th

in the SPH Music Masters Finale (aka, the German Battle of the Bands). We need your support!

The Representatives of Monkey Jack - German Battle of the Bands Finale

Authorships are

The Open Researcher and Contributor Identifier (ORCID) database is an invaluable resource that supports the unambiguous identification of researchers. However, its first party data dump is too complex, verbose, and unstandardized for many use cases. This post describes open source software I wrote that automates downloading, processing, and exporting ORCID into a more usable form. I put the results on Zenodo under the CC0 license.

Easier ORCID

The International Society of Biocuration (ISB) partners with the journal Database to get discounts for its members when they publish there. This means the ISB’s executive committee needs to send a member list to the journal’s editor.

Programmatic Access to a Wordpress User List

The Unified Medical Language System (UMLS) is a widely used biomedical and clinical vocabulary maintained by the United States National Library of Medicine. However, it is notoriously difficult to access and work with due to licensing restrictions and its complex download system. In the same vein as my previous posts about DrugBank and ChEMBL, this post describes open source software I’ve developed for downloading and working with this data.

Unlocking UMLS

I was recently nominated for the International Society for Biocuration’s Excellence in Biocuration Early Career Award (results will be announced on June 14

 th

!). This made me curious about how to model nominations and awards on Wikidata. In this post, I’ll describe how to curate awards, nominations, recipients, and how to make SPARQL queries to get them.

Modeling and Querying Awards in Wikidata

I’ve been working on improving reproducibility in the field of cheminformatics for some time now. For example, I’ve written posts about making data from DrugBank and ChEMBL more actionable. Over the last year, I’ve been preparing a concept with the editors of the Journal of Cheminformatics on how to include an assessment of reproducibility to reviews of manuscripts submitted to the journal.

Reproducibility Pilot in the Journal of Cheminformatics

Biopragmatics

[Graphviz](https://graphviz.org) is software for graph visualization
written in C. [PyGraphviz](https://pypi.org/project/pygraphviz) provides
a nice Python wrapper for it. The issue is that getting Python to know
about the C headers changes every few months. I'll try and keep this
blog post updated every time there are some changes.

# November 2024

These days, `pip install graphviz`{.language-plaintext
.highlighter-rouge} seemed to work but
`uv pip install graphviz`{.language-plaintext .highlighter-rouge} gave
the following:

:::: {.language-console .highlighter-rouge}
::: {.highlight}
``` highlight
$ uv pip install pygraphviz
Using Python 3.12.7 environment at /Users/cthoyt/.virtualenvs/orcid
Resolved 1 package in 597ms
error: Failed to prepare distributions
  Caused by: Failed to download and build `pygraphviz==1.14`
  Caused by: Build backend failed to build wheel through `build_wheel` (exit status: 1)

[stdout]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/scraper.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/testing.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
creating build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_repr_mimebundle.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
writing top-level names to pygraphviz.egg-info/top_level.txt
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-14.0-arm64-cpython-312/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-14.0-arm64-cpython-312/pygraphviz
clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/Users/cthoyt/Library/Caches/uv/builds-v0/.tmpKw7zNP/include -I/opt/homebrew/opt/python@3.12/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-14.0-arm64-cpython-312/pygraphviz/graphviz_wrap.o

[stderr]
warning: no files found matching '*.swg'
warning: no files found matching '*.png' under directory 'doc'
warning: no files found matching '*.html' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
pygraphviz/graphviz_wrap.c:9:9: warning: 'SWIG_PYTHON_STRICT_BYTE_CHAR' macro redefined [-Wmacro-redefined]
#define SWIG_PYTHON_STRICT_BYTE_CHAR
        ^
:2:9: note: previous definition is here
#define SWIG_PYTHON_STRICT_BYTE_CHAR 1
        ^
pygraphviz/graphviz_wrap.c:3023:10: fatal error: 'graphviz/cgraph.h' file not found
#include "graphviz/cgraph.h"
         ^~~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
  Caused by: This error likely indicates that you need to install a library that provides "graphviz/cgraph.h" for pygraphviz@1.14
```
:::
::::

Here's one solution that work (of the many possible ones):

:::: {.language-python .highlighter-rouge}
::: {.highlight}
``` highlight
$ export CFLAGS="-I$(brew --prefix graphviz)/include"
$ export LDFLAGS="-L$(brew --prefix graphviz)/lib"
$ uv pip install pygraphviz
Using Python 3.12.7 environment at /Users/cthoyt/.virtualenvs/orcid
Resolved 1 package in 2ms
   Built pygraphviz==1.14
Prepared 1 package in 908ms
Installed 1 package in 1ms
 + pygraphviz==1.14
```
:::
::::

There's also talk of using `--global-option`{.language-plaintext
.highlighter-rouge} to pass
`-I/opt/homebrew/opt/graphviz/include`{.language-plaintext
.highlighter-rouge} and
`-L/opt/homebrew/opt/graphviz/lib`{.language-plaintext
.highlighter-rouge}, but I couldn't figure this out for
`uv pip install`{.language-plaintext .highlighter-rouge}.

# 2023 Era

I was on Python 3.10 on a M2 Mac with macOS 13.
`pygraphviz`{.language-plaintext .highlighter-rouge} didn't have a
pre-built wheel for my systen so
`python -m pip install pygraphviz`{.language-plaintext
.highlighter-rouge} gave the following error:

:::: {.language-console .highlighter-rouge}
::: {.highlight}
``` highlight
$ python -m pip install pygraphviz
...
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/Users/cthoyt/.virtualenvs/indra/include -I/usr/local/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-13-x86_64-cpython-310/pygraphviz/graphviz_wrap.o
      pygraphviz/graphviz_wrap.c:3020:10: fatal error: 'graphviz/cgraph.h' file not found
      #include "graphviz/cgraph.h"
               ^~~~~~~~~~~~~~~~~~~
      1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]
```
:::
::::

I figured out based on the Homebrew troubleshooting in the docs
(https://pygraphviz.github.io/documentation/stable/install.html#homebrew)
that the following works:

:::: {.language-shell .highlighter-rouge}
::: {.highlight}
``` highlight
python -m pip install --use-pep517 \
    --config-setting="--global-option=build_ext" \
    --config-setting="--build-option=-I$(brew --prefix graphviz)/include/" \
    --config-setting="--build-option=-L$(brew --prefix graphviz)/lib/" \
    pygraphviz
```
:::
::::
