linkageio / minus80 Goto Github PK

Saw you were adding some cloud functionality. That is something I would use regularly so if you get to a good place and need any help testing lmk!

This can be fixed by updating ICU library for unicode

On Ubuntu:

# Download the source code
wget http://archive.ubuntu.com/ubuntu/pool/main/i/icu/icu_4.8.1.1.orig.tar.gz
# Extracting the tarball
tar xzf icu_4.8.1.1.orig.tar.gz
rm -rf icu_4.8.1.1.orig.tar.gz
cd icu/source
# configure and compile
./configure 
make
# Install
make install
# Clean up
rm -rf icu/

There should at least be basic tests for all the freezable methods.

If you make a lot of frozen arrays using the Freezable._bcolz_array method, each array gets saves as a file in the ~/.minus80/databases directory.

The correct behavior here should be a deeper directory structure:

.minus80/
    /databases
        /object
            /sqlite (relational)
            /bcolz (columnar)

Or something like this.

Hello Rob,
We are trying to install minus80 on our ubuntu server. I ran $pip3 install minus80 --prefix /project/chadm/Xiaotong/python_package, and we encounter the following issue.

...
Building wheel for minus80 (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wky9u_c3/minus80/setup.py'"'"'; file='"'"'/tmp/pip-install-wky9u_c3/minus80/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-dcnrqgi3
cwd: /tmp/pip-install-wky9u_c3/minus80/
Complete output (35 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/minus80
copying minus80/RawFile.py -> build/lib/minus80
copying minus80/Accession.py -> build/lib/minus80
copying minus80/GCPCloudData.py -> build/lib/minus80
copying minus80/RelationalDB.py -> build/lib/minus80
copying minus80/FireBaseCloudData.py -> build/lib/minus80
copying minus80/init.py -> build/lib/minus80
copying minus80/Tools.py -> build/lib/minus80
copying minus80/Project.py -> build/lib/minus80
copying minus80/Cohort.py -> build/lib/minus80
copying minus80/ColumnDB.py -> build/lib/minus80
copying minus80/Freezable.py -> build/lib/minus80
copying minus80/CloudData.py -> build/lib/minus80
copying minus80/Config.py -> build/lib/minus80
copying minus80/Exceptions.py -> build/lib/minus80
creating build/lib/minus80/cli
copying minus80/cli/minus80.py -> build/lib/minus80/cli
copying minus80/cli/init.py -> build/lib/minus80/cli
running egg_info
writing minus80.egg-info/PKG-INFO
writing dependency_links to minus80.egg-info/dependency_links.txt
writing entry points to minus80.egg-info/entry_points.txt
writing requirements to minus80.egg-info/requires.txt
writing top-level names to minus80.egg-info/top_level.txt
reading manifest file 'minus80.egg-info/SOURCES.txt'
writing manifest file 'minus80.egg-info/SOURCES.txt'
installing to build/bdist.linux-x86_64/wheel
running install
Installing apsw from GitHub using
error: [Errno 2] No such file or directory: 'pip'

ERROR: Failed building wheel for minus80
...

Can you help look into it? Please let me know if you need more details ([email protected]). Thanks.
Xiaotong

This can be solved by following the steps in Issue #3

Right now we have just add paths with a small check to see if files exist. This makes it so Accessions cannot be shared across machines and does not yield reproducing workflows. If possible, files should be stored as URLs or noted if the file is only specific to a certain machine.

A URL is broken down into a few pieces:

URI = scheme:[//authority]path[?query][#fragment]

Where authority is expressed as:

authority = [userinfo@]host[:port]