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Luis Pedro Coelho luispedro Fudan University Luxembourg & Shanghai http://luispedro.org

greenelab/covid19-review 81

A collaborative review of the emerging COVID-19 literature. Join the chat here:

BigDataBiology/macrel 17

Predict AMPs in (meta)genomes and peptides

luispedro/android-fuse 4

Mount an android device using FUSE

luispedro/base-user 2

dot files and the like so that I can set up a new computer with a couple of command line calls

luispedro/beiraproject 2

Beira Project Stuff

luispedro/alist 1

Append List in Haskell

issue openedBigDataBiology/macrel

Redirect log information

From the amphsphere-users mailing list:

I tested Macrel AMP detection on metagenome assemblies and was wondering, if a flag exists to save the log information. something like --logfile path/to/logfile.txt. The log is usually quite big

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pull request commentBigDataBiology/GMGC-mapper

Upload new version of index.ipynb

Hi @fernanda-ordonez

I believe this is no longer the most up to date set of changes, so closing, but let me know if I misunderstood

fernanda-ordonez

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create barnchluispedro/jug

branch : test_redis_on_ci

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ENH Add type hints This makes Jug Python 3.5+ only (we had kept 2.7 compatibility til version 2.0.x)

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TST BUG Fix testing Previously, CI would actually NOT detect failures as it would not be propagated to the exit code.

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ENH Add type hints This makes Jug Python 3.5+ only (we had kept 2.7 compatibility til now)

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TST BUG Fix testing Previously, CI would actually NOT detect failures as it would not be propagated to the exit code.

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TST BUG Fix testing Previously, CI would actually NOT detect failures as it would not be propagated to the exit code.

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BUG Fix mixing mapreduce & status --cache

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ENH Add type hints This makes Jug Python 3.5+ only (we had kept 2.7 compatibility til now)

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commit sha a98eaf0c3f33902010fde03e4c30ffc7a10368db

ENH Compatibility with Python 3.8 Add testing for Python 3.8 too

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MIN Remove use of deprecated name

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BUG Fix for Python 3.8 Python 3.8 introduced `pickle.PickleBuffer` and this would trigger an error in Jug

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commit sha bc73e50939c6353faef6f937e1b65ef3c5266be5

ENH Jug will no longer support Python 2.7

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MIN Python 2 is not supported

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MIN DOC Update Copyright statement Update date & email address

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BUG Fix mixing mapreduce & status --cache

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ENH Add type hints This makes Jug Python 3.5+ only (we had kept 2.7 compatibility til now)

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BUG Fix mixing mapreduce & status --cache

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BUG Fix mixing mapreduce & status --cache

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issue openedngless-toolkit/ng-meta-profiler

Make the mOTUs 2 human profiler the main one

The recommendation should be to use the state-of-the-art.

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Luis Pedro Coelho

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MIN Python 2 is not supported

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MIN DOC Update Copyright statement Update date & email address

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create barnchBigDataBiology/ampsphere-frontend

branch : master

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created repositoryBigDataBiology/ampsphere-frontend

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issue commentluispedro/sparcc

Syntax errors in sparCC.py

No, sorry.

Up4itat24

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issue closedBigDataBiology/macrel

Bioconda release for Mac OS

Hi,

Any chance that you are considering MACREL release for macOS?

Thanks

Somak

closed time in 7 days

somakchowdhury

issue commentBigDataBiology/macrel

Bioconda release for Mac OS

We've finally resolved this issue and macrel is available for osx on bioconda!

somakchowdhury

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issue closedBigDataBiology/macrel

conda install -c bioconda macrel not working

hello, the conda install command doesn't work and it gives the following message. could I ask for help?


Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  • macrel

Current channels:

  • https://conda.anaconda.org/bioconda/osx-64
  • https://conda.anaconda.org/bioconda/noarch
  • https://conda.anaconda.org/conda-forge/osx-64
  • https://conda.anaconda.org/conda-forge/noarch
  • https://repo.anaconda.com/pkgs/main/osx-64
  • https://repo.anaconda.com/pkgs/main/noarch
  • https://repo.anaconda.com/pkgs/r/osx-64
  • https://repo.anaconda.com/pkgs/r/noarch
  • https://conda.anaconda.org/r/osx-64
  • https://conda.anaconda.org/r/noarch
  • https://conda.anaconda.org/anaconda-fusion/osx-64
  • https://conda.anaconda.org/anaconda-fusion/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

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ssyim

issue commentBigDataBiology/macrel

conda install -c bioconda macrel not working

Macrel is now available on mac osx from conda

ssyim

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issue commentluispedro/sparcc

Syntax errors in sparCC.py

I probably meant to fix something/improve something on the code, but I don't remember what it could be

Up4itat24

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issue commentluispedro/sparcc

Syntax errors in sparCC.py

Hi, This is not the main sparCC repository. To be frank, I don't remember why I have a copy as it seems to be just an older version of the code. I will delete later

Up4itat24

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issue closedluispedro/sparcc

Syntax errors in sparCC.py

Hello!

I'm relatively new to python so my apologies if this is a lame question. Im hoping to use sparCC for doing correlations on my ITS compositional data. I downloaded the scripts from the repository and am trying to go through the example with the fake data set provided.

But when I run python SparCC.py example/fake_data.txt -i 5 --cor_file=example/basis_corr/cor_sparcc.out

I get the following error:

File "SparCC.py", line 181 raise ValueError 'Can not detect correlations between compositions of <4 components (%d given)' %k
^ SyntaxError: invalid syntax

I previously got a syntax error when line 181 read raise ValueError, 'Can not detect correlations between compositions of <4 components (%d given)' %k

and it did not like the comma after ValueError. Now after removing that it doesn't like the quotation closing the string.

I would really appreciate any help on fixing the syntax errors I'm getting!

Thanks!

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Up4itat24

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updated v2.0.3

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PR merged conda-forge/jug-feedstock

jug v2.0.3

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Analysis of the source code shows no discrepancy between the library's imports and the package's stated requirements in the meta.yaml.

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created tagluispedro/jug

tagv2.0.3

Parallel programming with Python

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Luis Pedro Coelho

commit sha 20ec019729c1e40c5fd8706316992b466b03604c

RLS Version 2.0.3 Fix for Python 3.8

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pull request commentbioconda/bioconda-recipes

Macrel can build on OSX now

There are missing dependencies on Mac OS X for any version other than Python 3.8.

luispedro

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Luis Pedro Coelho

commit sha bc73e50939c6353faef6f937e1b65ef3c5266be5

ENH Jug will no longer support Python 2.7

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Luis Pedro Coelho

commit sha 3f7ccb8cdf37439bbc44c2b7039444f8886ff544

MIN+BUG Only use memoryview on Python 3 Version checking is inelegant, but this for Jug versions post 2.0, we will no longer support Python 2.7

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create barnchluispedro/jug

branch : v2.0.x

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commit sha d9871668193cacccc2eaa96484c3a43a724819a1

BUG Fix for Python 3.8 Python 3.8 introduced `pickle.PickleBuffer` and this would trigger an error in Jug

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Luis Pedro Coelho

commit sha a98eaf0c3f33902010fde03e4c30ffc7a10368db

ENH Compatibility with Python 3.8 Add testing for Python 3.8 too

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MIN Remove use of deprecated name

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create barnchluispedro/diskhash

branch : update_test_versions

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commit sha 4fe2547bad3e1bc95e9a9d5df12a6e3913b27574

TST MIN Migrate to travis-ci.com

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dvzubarev

commit sha 5ab0f1aebc89a6eb7e008bbc48e1df542858aa51

MIN replace is_pod with is_trivially_copyable `is_trivially_copyable` is the correct requirement, namely that the object is `memcpy()`able. In fact, `is_pod` has been deprecated as it was too broad close #12

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PR merged luispedro/diskhash

Replace is_pod with is_trivially_copyable

resolves #12

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dvzubarev

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issue closedluispedro/diskhash

Question about POD data

Hi, thank you for this library. I was trying to use c++ API of this library for this data: key = uint32_t and my value is

struct temp_t {
    std::uint32_t    _cnt   =0 ;
    std::uint32_t    _cnt2 =0;
};

But it fails to compile, because of static_assert:

 static_assert(std::is_pod<T>::value,
            "DiskHash only works for POD (plain old data) types that can be mempcy()ed around");

My struct is not POD because it has user-defined constructor. But, I believe it still can be memcpyed. Maybe its better to replace std::is_pod with std::is_standard_layout? What do you think? Also is_pod is deprecated in c++20.

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dvzubarev

pull request commentluispedro/diskhash

Replace is_pod with is_trivially_copyable

Thanks!

dvzubarev

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issue commentluispedro/diskhash

Question about POD data

I think you're right, std::is_pod is too restrictive, but the right property is probably std::is_trivially_copyable.

Can you do a PR?

dvzubarev

comment created time in 8 days

pull request commentbioconda/bioconda-recipes

Macrel can build on OSX now

There are no changes to this package per se. It was just blocked (for OSX) on a dependency before and can now be used there.

luispedro

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pull request commentbioconda/bioconda-recipes

Macrel can build on OSX now

@BiocondaBot please add label

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Luis Pedro Coelho

commit sha 1e2d380e8e6bd7e40fddc8c665547b8698c4e1f6

ENH OSX dependencies only available for Python 3.8

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PR opened bioconda/bioconda-recipes

Macrel can build on OSX now

After merging https://github.com/bioconda/bioconda-recipes/pull/24262, NGLess OSX packages are available and macrel can be built on OSX

Ping https://github.com/BigDataBiology/macrel/issues/19 & https://github.com/BigDataBiology/macrel/issues/21

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

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branch : macrel_on_osx

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MIN Tweak English translation

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ENH ISCB EDI committee+scientific communication

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ENH Split publications by 1st/corresponding+rest

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BLD Update to latest nix for building

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pull request commentbioconda/bioconda-recipes

Ngless v1.2.0 macosx build

@BiocondaBot please add label

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DAT Fix hash file

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DAT Update hashes

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commit sha 600bb827c374d8802f49b6466d437a198b2787cf

BUG+RFCT Use the whole training dataset The testset is pre-built to already be non-overlapping (in the 80% sense), no need to split again Also, simplify code

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Merge pull request #1 from luispedro/cleanup Cleanup

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Add files via upload - Add script to generate figure 4

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Update README.md correct citation and add figure 4 rendering script

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Add script to generate plots of figure 3 Add R script to generate plots of figure 3

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Update README.md add generation of figure 3

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Add figure 4 data source Add data source for figure 4 with all informations relative to simulated metagenomes run to benchmark Macrel

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Changed internal data

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ENH Load data from Excel file Keep it DRY

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Ngless v1.2.0 macosx build

Update NGLess recipe

For Linux, fixes build.sh to run on newer conda.

For Mac OS X, installs the prebuilt binaries (as the approach used on Linux seems to fail with some OSX-internal errors).

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Bumps node-sass from 3.3.3 to 4.14.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/sass/node-sass/releases">node-sass's releases</a>.</em></p> <blockquote> <h2>v4.14.1</h2> <h3>Community</h3> <ul> <li>Add GitHub Actions for Alpine CI (<a href="https://github.com/nschonni">@nschonni</a>, <a href="https://github-redirect.dependabot.com/sass/node-sass/issues/2823">#2823</a>)</li> </ul> <h3>Fixes</h3> <ul> <li>Bump sass-graph@2.2.5 (<a href="https://github.com/xzyfer">@xzyfer</a>, <a href="https://github-redirect.dependabot.com/sass/node-sass/issues/2912">#2912</a>)</li> </ul> <h2>Supported Environments</h2> <table> <thead> <tr> <th>OS</th> <th>Architecture</th> <th>Node</th> </tr> </thead> <tbody> <tr> <td>Windows</td> <td>x86 & x64</td> <td>0.10, 0.12, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14</td> </tr> <tr> <td>OSX</td> <td>x64</td> <td>0.10, 0.12, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14</td> </tr> <tr> <td>Linux*</td> <td>x86 & x64</td> <td>0.10, 0.12, 1, 2, 3, 4, 5, 6, 7, 8**, 9**, 10**^, 11**^, 12**^, 13**^, 14**^</td> </tr> <tr> <td>Alpine Linux</td> <td>x64</td> <td>6, 8, 10, 11, 12, 13, 14</td> </tr> <tr> <td>FreeBSD</td> <td>i386 amd64</td> <td>10, 12, 13</td> </tr> </tbody> </table> <p>Linux support refers to Ubuntu, Debian, and CentOS 5+ ** Not available on CentOS 5 ^ Only available on x64</p> <h2>v4.14.0</h2> <h3>Features</h3> <ul> <li>Add Node 14 support (<a href="https://github.com/nschonni">@nschonni</a>, <a href="https://github-redirect.dependabot.com/sass/node-sass/issues/2895">#2895</a>)</li> </ul> <h3>Fixes</h3> <ul> <li>Reporting wrong LibSass version (<a href="https://github.com/saper">@saper</a>, <a href="https://github-redirect.dependabot.com/sass/node-sass/issues/2621">#2621</a>)</li> </ul> <h2>Supported Environments</h2> <table> <thead> <tr> <th>OS</th> <th>Architecture</th> <th>Node</th> </tr> </thead> <tbody> <tr> <td>Windows</td> <td>x86 & x64</td> <td>0.10, 0.12, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14</td> </tr> <tr> <td>OSX</td> <td>x64</td> <td>0.10, 0.12, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14</td> </tr> <tr> <td>Linux</td> <td>x86 & x64</td> <td>0.10, 0.12, 1, 2, 3, 4, 5, 6, 7, 8**, 9**, 10**^, 11**^, 12**^, 13**^, 14**^</td> </tr> <tr> <td>Alpine Linux</td> <td>x64</td> <td>6, 8, 10, 11, 12, 13, 14</td> </tr> <tr> <td>FreeBSD</td> <td>i386 amd64</td> <td>10, 12, 13</td> </tr> </tbody> </table> <p>*Linux support refers to Ubuntu, Debian, and CentOS 5+ ** Not available on CentOS 5 ^ Only available on x64</p> <h2>v4.13.1</h2> <h3>Community</h3> <ul> <li>Fix render example syntax (<a href="https://github.com/ZoranPandovski">@ZoranPandovski</a> , <a href="https://github-redirect.dependabot.com/sass/node-sass/issues/2787">#2787</a>)</li> </ul> <!-- raw HTML omitted --> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/sass/node-sass/blob/master/CHANGELOG.md">node-sass's changelog</a>.</em></p> <blockquote> <h2>v4.14.0</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.14.0">https://github.com/sass/node-sass/releases/tag/v4.14.0</a></p> <h2>v4.13.1</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.13.1">https://github.com/sass/node-sass/releases/tag/v4.13.1</a></p> <h2>v4.13.0</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.13.0">https://github.com/sass/node-sass/releases/tag/v4.13.0</a></p> <h2>v4.12.0</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.12.0">https://github.com/sass/node-sass/releases/tag/v4.12.0</a></p> <h2>v4.11.0</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.11.0">https://github.com/sass/node-sass/releases/tag/v4.11.0</a></p> <h2>v4.10.0</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.10.0">https://github.com/sass/node-sass/releases/tag/v4.10.0</a></p> <h2>v4.9.4</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.9.4">https://github.com/sass/node-sass/releases/tag/v4.9.4</a></p> <h2>v4.9.3</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.9.3">https://github.com/sass/node-sass/releases/tag/v4.9.3</a></p> <h2>v4.9.2</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.9.2">https://github.com/sass/node-sass/releases/tag/v4.9.2</a></p> <h2>v4.9.1</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.9.1">https://github.com/sass/node-sass/releases/tag/v4.9.1</a></p> <h2>v4.9.0</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.9.0">https://github.com/sass/node-sass/releases/tag/v4.9.0</a></p> <h2>v4.8.3</h2> <p><a href="https://github.com/sass/node-sass/releases/tag/v4.8.3">https://github.com/sass/node-sass/releases/tag/v4.8.3</a></p> <h2>v4.8.2</h2> <!-- raw HTML omitted --> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/sass/node-sass/commit/0d6c3cc36a5362e83529d901484b0bbf3e96de81"><code>0d6c3cc</code></a> 4.14.1</li> <li><a href="https://github.com/sass/node-sass/commit/1cc626373196500b288f487e1507926066f3e406"><code>1cc6263</code></a> Bump sass-graph@2.2.5 (<a href="https://github-redirect.dependabot.com/sass/node-sass/issues/2915">#2915</a>)</li> <li><a href="https://github.com/sass/node-sass/commit/aa193f6334e45ae065cc64d67498acfad9fad4d9"><code>aa193f6</code></a> chore: Add GitHub Actions for Alpine CI</li> <li><a href="https://github.com/sass/node-sass/commit/eac343c6cc39abff153b2c8e9cc0d6b8351c8a8f"><code>eac343c</code></a> 4.14.0</li> <li><a href="https://github.com/sass/node-sass/commit/bbeb78cab873b12fc4b98358b62090e6fbc9b400"><code>bbeb78c</code></a> Update changelog</li> <li><a href="https://github.com/sass/node-sass/commit/1210aabc65ed445263dac5041ad735e3a35ae600"><code>1210aab</code></a> Fix <a 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issue closedluispedro/mahotas

Can't import mahotas.polygon on AWS Ubuntu 20.04 when inside CellProfiler

I think this is more likely a CellProfiler issue or a "missing ubuntu library" issue, but as I'm less familiar with mahotas import errors hoping the solution will be obvious to someone here. Otherwise, feel free to close.

Detailed here, but I set up a clean AWS Ubuntu 20.04 instance to run some tests per these instructions. Mahotas seems to install fine, and the following runs without error in python 3.8.2.

>>> import mahotas
>>> mahotas.__version__
'1.4.11'
>>> import skimage.data
>>> a = skimage.data.camera()
>>> mahotas.polygon.line((0,0),(1,1),a)

The two installed CellProfiler modules that require mahotas (or mahotas.features) fail to import it, with identical failed import strings:

Could not load cellprofiler.modules.watershed
Traceback (most recent call last):
  File "/home/ubuntu/.local/lib/python3.8/site-packages/cellprofiler_core/utilities/core/modules/__init__.py", line 71, in add_module
    m = __import__(mod, globals(), locals(), ["__all__"], 0)
  File "/home/ubuntu/CellProfiler/cellprofiler/modules/watershed.py", line 2, in <module>
    import mahotas
  File "/home/ubuntu/.local/lib/python3.8/site-packages/mahotas/__init__.py", line 83, in <module>
    from . import polygon
  File "/home/ubuntu/.local/lib/python3.8/site-packages/mahotas/polygon.py", line 8, in <module>
    from . import _convex
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf3 in position 0: invalid continuation byte

Any ideas? Thanks!

closed time in 25 days

bethac07

issue commentluispedro/mahotas

Can't import mahotas.polygon on AWS Ubuntu 20.04 when inside CellProfiler

Thanks for the test outputs. I think from mahotas' POV, everything is working so I am closing here

bethac07

comment created time in 25 days

issue commentluispedro/mahotas

Can't import mahotas.polygon on AWS Ubuntu 20.04 when inside CellProfiler

Sorry, this seems strange: if mahotas imports OK when you run it on the shell, it seems that it should also work on from cellprofiler

Can you run:

import mahotas
mahotas.test()

? This may require pytest to be available, so it may fail for that reason.

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