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Bo BoPeng Baylor College of Medicine Houston, TX, USA http://bioworkflows.com

jupyterlab/jupyterlab 10253

JupyterLab computational environment.

BoPeng/simuPOP 19

A general-purpose forward-time population genetics simulation environment.

gaow/SEQPower 2

Power Analysis and Sample Size Estimation Software for Sequence Based Association Studies

BoPeng/simuPOP-examples 1

Collection of sample scripts in simuPOP

vatlab/sos-papermill 1

Batch executor of sos notebooks

bioworkflows/bioworkflows-help 0

Public issue tracker for bioworkflows.com

bioworkflows/django-file-form 0

Django-file-form helps you to write forms with a pretty ajax upload

bioworkflowstest/covid-19-county-R0 0

County level data for the covid-19 R0 estimator

BoPeng/django-file-form 0

Django-file-form helps you to write forms with a pretty ajax upload

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Introduce the concept of vincinity

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issue commentvatlab/varianttools

KING 2.2.4

I am not an KING expert and do not know what is going on here? DId you contact the author of KING?

Yomiran

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Add paramters sensitivity and specificity to pcrtest

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Release outbreak simulator 0.3.4

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Add test for plugin remove

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issue closedvatlab/sos

Clear <defunct> workers

Right now the master process sends a None signal to workers and let them kill themselves. However, this creates <defunct> processes because p.join() is not properly called, as described here.

The problem here is that when some worker says I want work, and the master says I do not have any, please sucide, the master does not really know which worker is idle, and cannot join() it explicitly. Perhaps the SIGCHILD signal should be used.

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issue closedBoPeng/django-managed-tasks

Please comment on the design, and help test the module if possible

@QbasicFan : This module has been under development in a production environment. It has been tested (with a coverage of about 95%) and used for another project, and I have just copied the code to this project. The original source will continue to evolve with code migrating to this project, but the mother project will remove the internal copy and use this project once it is mature.

The tests use pytest and works on our environment but I have not figured out how to make it run independently, and I have no experience with tox, which was set up by cookiecutter. I also have not written any documentation (besides the README). I would really appreciated it if you could review the package, set up the tests etc, even write some documentation if you have some time. Many thanks in advance.

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BoPeng

issue closedbioworkflows/django-file-form

Add a checkbox for each uploaded file.

For bioworkflows, we need to allow users to choose one of the files as the primary file to be shown for the project. This requires us to add a checkbox (mutually exclusive) to each of the uploaded file, be it real or placeholder.

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BoPeng

pull request commentbioworkflows/django-file-form

Upload event

merged by upstream.

BoPeng

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sos v0.21.15 (#52) * updated v0.21.15 * MNT: Re-rendered with conda-build 3.20.2, conda-smithy 3.7.10, and conda-forge-pinning 2020.09.17.18.26.02 Co-authored-by: regro-cf-autotick-bot <circleci@cf-graph.regro.github.com>

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sos v0.21.14

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Analysis of the source code shows a discrepancy between the library's imports and the package's stated requirements in the meta.yaml.

Packages found by inspection but not in the meta.yaml:

  • numpy
  • ipykernel
  • spyder
  • celery
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  • sos-notebook
  • pandas

Packages found in the meta.yaml but not found by inspection:

  • ptyprocess
  • pydot
  • pydotplus
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sos v0.21.15

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Closes: #51

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<sub>This PR was created by the regro-cf-autotick-bot. The regro-cf-autotick-bot is a service to automatically track the dependency graph, migrate packages, and propose package version updates for conda-forge. If you would like a local version of this bot, you might consider using rever. Rever is a tool for automating software releases and forms the backbone of the bot's conda-forge PRing capability. Rever is both conda (conda install -c conda-forge rever) and pip (pip install re-ver) installable. Finally, feel free to drop us a line if there are any issues! This PR was generated by https://circleci.com/gh/regro/circle_worker/49976, please use this URL for debugging</sub>

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Analysis of the source code shows a discrepancy between the library's imports and the package's stated requirements in the meta.yaml.

Packages found by inspection but not in the meta.yaml:

  • ipykernel
  • spyder
  • celery
  • pandas
  • sos-notebook
  • numpy
  • ipython

Packages found in the meta.yaml but not found by inspection:

  • pydot
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Update report

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issue closedvatlab/sos

SGE issue with multiple jobs per node

On our cluster system, with trunk_size larger than 1, we run into an error. Here is the script that triggers it:

[STEP_1]
A = [1,2,3,4,5,6]
input: for_each = "A"
task: trunk_workers = 1, trunk_size = 2, walltime = '4h',  mem = '1G', tags = f'{step_name}'
bash: expand = "$[ ]"
        echo $[_A]

and job template: https://github.com/cumc/bioworkflows/blob/master/GWAS/csg.yml, with command to run:

sos run test.sos -c GWAS/csg.yml -q csg -v4

Error message below shows the line in question:

INFO: M2_571b7d27504106d1 started
  File "/home/gw2411/miniconda3/lib/python3.8/site-packages/sos/__main__.py", line 2521, in main
    args.func(args, workflow_args)
Traceback (most recent call last):
  File "/home/gw2411/miniconda3/lib/python3.8/site-packages/sos/__main__.py", line 2521, in main
    args.func(args, workflow_args)
  File "/home/gw2411/miniconda3/lib/python3.8/site-packages/sos/__main__.py", line 1363, in cmd_execute
    exit_code.append(executor.execute(task))
  File "/home/gw2411/miniconda3/lib/python3.8/site-packages/sos/task_executor.py", line 89, in execute
    res = self.execute_master_task(task_id, params, runtime,
  File "/home/gw2411/miniconda3/lib/python3.8/site-packages/sos/task_executor.py", line 387, in execute_master_task
    n_nodes, n_procs = self._parse_num_workers(env.config['worker_procs'])
  File "/home/gw2411/miniconda3/lib/python3.8/site-packages/sos/task_executor.py", line 560, in _parse_num_workers
    n_workers = int(val.rsplit(':', 1)[-1])
ValueError: invalid literal for int() with base 10: 'UNDEFINED'

So I printed near line 560 the variable num_workers. It says:

['node42:1:all.q@node42:UNDEFINED']

@BoPeng I guess the number you would like to extract is the 1 right after the first node42. But unfortunately the convention here is different. Is there are more robust approach to this?

closed time in 4 days

gaow

issue commentvatlab/sos

SGE issue with multiple jobs per node

sos 0.21.15 is released for this fix.

gaow

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Release sos 0.21.15

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issue commentvatlab/sos

SGE issue with multiple jobs per node

Could you try again? You can manually edit the file in place if it is difficult to compile the master branch of sos on cluster nodes.

gaow

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Fix handling of PE_HOSTFILE for Sun Grid #1401

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push eventconda-forge/sos-pbs-feedstock

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commit sha 9e5d67f8760643f9a6b633948f7642b7378b2ec2

updated v0.20.8

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commit sha 60cf51b9effd7e40f006944c41ac675fae5b2b42

Merge pull request #9 from regro-cf-autotick-bot/0.20.8_h6a2686 sos-pbs v0.20.8

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PR merged conda-forge/sos-pbs-feedstock

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sos-pbs v0.20.8

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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.

+6 -6

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issue commentvatlab/sos

PBS issue with multiple jobs per node

So it is SGE, something I was not able to test. I will submit a patch this afternoon.

gaow

comment created time in 4 days

issue commentvatlab/sos

PBS issue with multiple jobs per node

No. The code only triggers when the task is submitted and executed by the cluster, so you will have to add export stuff in the template. I can fix the bug from your description of it is difficult to do.

gaow

comment created time in 4 days

issue closedansible/ansible-jupyter-kernel

Compatibility with MacOSX and python 3.7

Describe the bug ansible kernel hangs under MacOSX and python 3.7.

To Reproduce Create a fresh conda environent, and ansible kernel does not work.

$ conda create -n ansible python=3.7
$ pip install ansible-kernel
$ python -m ansible_kernel.install
$ jupyter notebook
[W 11:50:09.718 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[I 11:50:09.720 NotebookApp] The port 8888 is already in use, trying another port.
[I 11:50:09.720 NotebookApp] The port 8889 is already in use, trying another port.
[I 11:50:09.728 NotebookApp] Serving notebooks from local directory: /Users/bpeng1
[I 11:50:09.728 NotebookApp] The Jupyter Notebook is running at:
[I 11:50:09.728 NotebookApp] http://bcbm-bpeng.mdanderson.edu:8890/
[I 11:50:09.728 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 11:50:14.887 NotebookApp] Creating new notebook in
[I 11:50:15.881 NotebookApp] Kernel started: cae4aef6-83f6-4f08-89ec-1d9e3262f363
/Users/bpeng1/anaconda3/envs/ansible/lib/python3.7/site-packages/ansible_kernel/modules.py:4: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  modules = yaml.load(f.read())
/Users/bpeng1/anaconda3/envs/ansible/lib/python3.7/site-packages/ansible_kernel/module_args.py:4: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  module_args = yaml.load(f.read())
[W 11:51:15.951 NotebookApp] Timeout waiting for kernel_info reply from cae4aef6-83f6-4f08-89ec-1d9e3262f363
[I 11:52:16.453 NotebookApp] Saving file at /Untitled.ipynb
^C[I 11:52:52.442 NotebookApp] interrupted

Screenshots image

Desktop (please complete the following information):

  • OS: MacOSX
  • Browser Chrome
  • Jupyter Notebook Version: 6.0.1

closed time in 4 days

BoPeng

issue commentansible/ansible-jupyter-kernel

Compatibility with MacOSX and python 3.7

https://github.com/ansible/ansible-jupyter-kernel/issues/84

Seems that Ansible kernel is no longer maintained (no commits and bug fix for two years). I will re-open this ticket after the aforementioned ticket from upstream is addressed.

BoPeng

comment created time in 4 days

issue closedvatlab/sos-notebook

xonsh Kernel

Hello Bo Peng, thanks for sharing Sos. Would it be possible to add Xonsh as an SoS sub kernel?

I see you use the metakernel/Calysto bash as a base for your bash sub kernel and that there is a metakernel/Calysto xonsh as well, so maybe it would be fairly easy to add xonsh?

https://nbviewer.jupyter.org/github/Calysto/xonsh_kernel/tree/master/

regards

closed time in 4 days

WardThomas

issue commentvatlab/sos-notebook

xonsh Kernel

@WardThomas I am closing this ticket since the upstream has not been fixed. I will re-open this ticket if Calysto/xonsh_kernel#13 is fixed.

WardThomas

comment created time in 4 days

issue closedvatlab/sos-notebook

how to interrupt a sub kernel?

Can't find a way to interrupt the sub-kernel.

closed time in 4 days

kundeng

issue commentvatlab/sos-notebook

how to interrupt a sub kernel?

I think the problem here is that it is not easy to determine if sos or one of its subkernels is being interrupted.

kundeng

comment created time in 4 days

issue closedvatlab/sos-notebook

bash sub-kernel evaluation queued for a very long time

for i in seq 1 10 do echo $i done

very simple loop, not sure why it gets queued for a very long time. I restarted the meta-kernel (along with all sub kernels) and rerun and it worked. So not sure what happened there.

closed time in 4 days

kundeng

issue commentvatlab/sos-notebook

bash sub-kernel evaluation queued for a very long time

Cannot reproduce.

kundeng

comment created time in 4 days

push eventvatlab/sos-pbs

Bo Peng

commit sha f1404895ccc5aac7e9ee7b3315adee81b16379d2

Release sos-pbs 0.20.8

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issue commentvatlab/sos

PBS issue with multiple jobs per node

Could you define SOS_DEBUG=WORKER and see the output of the following function?

https://github.com/vatlab/sos/blob/master/src/sos/utils.py#L1860

I just want to understand what variables are defined by your cluster.

gaow

comment created time in 4 days

issue commentvatlab/sos

PBS issue with multiple jobs per node

Is this standard PBS? Looks like this should be defined by the cluster environment variable and UNDEFINED should usually be a number?

gaow

comment created time in 4 days

issue closedvatlab/sos

`pytest` for sos-pbs?

I'm reporting an issue with PBS job submission but before the main issue let me point out this line that I see when I use -v4:

INFO: Running STEP_1: 
DEBUG: Failed to load workflow engine pbs: No module named 'pytest'
DEBUG: submit M2_571b7d27504106d1: qsub ~/.sos/tasks/M2_571b7d27504106d1.sh
INFO: M2_571b7d27504106d1 submitted to csg with job id 730353

nothing fails but it is just a nuisance -- pointing it out in case this can be fixed quickly

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gaow

issue commentvatlab/sos

`pytest` for sos-pbs?

Fixed. Not sure how it landed there.

gaow

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commit sha 9c01ba99438724b9c6ac688bc717f9872dbb6d35

Remove dependency on pytest from sos-pbs vatlab/sos#1400

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issue closedvatlab/sos-notebook

Show more information about kernel and language module used.

vatlab/sos-matlab#9 mentioned a problem with the existence of multiple versions of language modules. I have also been confused by this, and also the use of kernelspec from another conda environment.

More specifically, some kernelspec uses relative path (e.g. R) so that a different version of R will be used when you switch conda environment, but some kernelspec uses absolute path (e.g. '/path/to/julia`) so the same interpreter will be used after switching conda environment. It can be really confusing because everything looks ok outside (in conda), but jupyter would not work correctly.

What made things worse are

  1. Jupyter itself can be installed in base
  2. kernelspec can be installed global and conda-specific locations

It can be helpful if sos can display exact interpreter, kernelspec, and language module to make it easier to debug such problems.

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BoPeng

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commit sha 9d431c349a77e2c4961f47776df1393389a19b44

Fix magic use with -r

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commit sha bfdac0f92168913bc3fb142e1e2e375da6a3333d

Show more details of available kernels #291

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issue commentvatlab/sos-notebook

Use jupyter gateway to support remote jupyter server or server in docker images

@stevehaertel My problem is that there does not seem to be a "standard" way to use remote kernels. I mean, if you can show me

  1. How the remote kernel is set up.
  2. How local server is set up to use the remote kernel (outside of SoS).

I can see how sos-notebook can be configured to talk to the remote kernel.

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issue commentmbraak/django-file-form

Callbacks or event emitter

The only problem with this is that addUpload events for the initial uploads are not handled. Because the events are already emitted after initUploadFields is called.

Then it will be difficult to implement our example, which has placeholders.

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issue commentmbraak/django-file-form

Callbacks or event emitter

Note that documentation on initUploadFields misses option eventEmitter.

options (optional)
    callbacks: callbacks for things like upload progress and errors.
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issue commentmbraak/django-file-form

Release a new version

With #359 and #361 open? I understand the event API is considered to be experimental though.

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issue commentmbraak/django-file-form

Callbacks or event emitter

Yes, it does appear to be some duplicated functionality here.

As far as I can tell, callbacks are only for Upload, so they do not yet work for S3, placeholder, and reload of form. Of course more callbacks can be added, at least to S3, but the advantage of signal is that the same signal could be emitted by different mechanisms ( e.g. addUpload by placeholder, S3, tus etc), whereas multiple callbacks would have to be defined for each of them. (I am likely wrong here).

On the other hand the event interface does not yet handle onProgress, onCancel, onError etc, which I assume would be easy to add.

So

Possible solution is to use the callbacks option for all events.

I agree, but the events mechanism appears to be more powerful, and more modern.

The goal is to not break existing code.

If so decided, we could deprecate callbacks by removing its documentation but keeping the implementation for backward compatibility.

Possible step: see if the new events can be handled by the callbacks option.

Not possible without expanding callbacks, as far as I can tell.

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PR opened mbraak/django-file-form

Add event uploadComplete

I find it better to add my widget (or not add at all) after the upload is completed. Could you add this event?

+60 -56

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PR opened bioworkflows/django-file-form

Upload event
+80 -97

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issue commentkrassowski/jupyterlab-lsp

How to implement LSP for a multi-language kernel (SoS)?

Yes, this is on my TODO list, even relatively high, but I am swamped with other obligations (covid related projects, not surprisingly) and have not been able to work on this.

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issue commentvatlab/sos-notebook

can't replicate bash flow behavior from docs

Yes, the %capture and %expand magics work for any kernel, but %get and %put only work for kernels with related language module because they need to understand the datatypes of the underlying languages. If you have sos-notebook installed and working, I suppose your system admin would not mind installing sos-bash, sos-python etc to make the sos environment more useful.

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issue closedvatlab/sos-notebook

can't replicate bash flow behavior from docs

In the docs, there is a simple intro for passing variables back and forth from Bash to SoS. (I'm talking about this page: https://vatlab.github.io/sos-docs/doc/user_guide/sos_bash.html#Bash- However, I cannot replicate it!

This works: [inside bash kernel] %capture stdout --to bash_output echo "I am from Bash"

[inside SoS kernel] bash_output

This works fine and I get expected print output. However, the following doesn't work (screenshot attached) [inside bash kernel] b='Hello from Bash' echo $b

[inside SoS kernel] %get b --from Bash b

[0]:

NameError Traceback (most recent call last) script_1290943559931815799 in <module> ----> b

NameError: name 'b' is not defined

Screen Shot 2020-09-09 at 2 52 48 PM

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issue commentvatlab/sos-notebook

can't replicate bash flow behavior from docs

Did you install sos-bash?

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PR opened mbraak/django-file-form

Update README

Noticed that the header was incorrectly formatted.

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Add events (#341) * Add eventemitter and addUpload event * Handle event in example code * Add removeUpload event * Use eventEmitter parameter. This way events for the initial uploads can be handled * Update example code * Build js * Update example: listen to events before initialing the form * Fix return * Add events metadata (#344) * Update README for usage * Passing meta data between front and backend * Fix example * Update README * Custom widget: move descriptionChanged code inside handler * Add metaDataField to addUpload event * Use metaDataField in custom widget * Build js * Check if metadata exists before setting it * Correctly set description in metadata Co-authored-by: Bo Peng <ben.bog@gmail.com> * Correctly set metaDataField * Update example * Build js * Introduce emitEvent function * Add fileName parameter * Use fileName parameter in example * Build js * Example: add input after filename * Add docs; also update changelog * Update readme Co-authored-by: Bo Peng <ben.bog@gmail.com>

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issue closedmbraak/django-file-form

Anything similar to s3_upload_dir for tus upload?

I am using s3_upload_dir = self.request.user.username to separate uploads from multiple users and found it convenient.Perhaps I have missed something obvious but I am wondering if django-file-form has a similar mechanism for adding form specific subdirectory for tus upload. If not, can we add something to balance the feature sets for tus and s3 uploads?

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issue commentmbraak/django-file-form

Keeping directory structure

Something like the following

diff --git a/frontend/src/drop_area.ts b/frontend/src/drop_area.ts
index 5dedcdd..d27e27c 100644
--- a/frontend/src/drop_area.ts
+++ b/frontend/src/drop_area.ts
@@ -20,6 +20,7 @@ const getFilesFromFileSystemEntries = async (
   for await (const entry of entries) {
     if (entry.isFile) {
       const file = await getFileFromFileEntry(entry as FileSystemFileEntry);
+      Object.defineProperty(file, 'path', {value: entry.fullPath.slice(1) })
       result.push(file);
     } else if (entry.isDirectory) {
       const entriesFromDirectory = await getEntriesFromDirectory(
diff --git a/frontend/src/upload_file.ts b/frontend/src/upload_file.ts
index 16f1150..5803eab 100644
--- a/frontend/src/upload_file.ts
+++ b/frontend/src/upload_file.ts
@@ -246,7 +246,7 @@ class UploadFile {
     }

     upload.start();
-    renderer.addNewUpload(filename, uploadIndex);
+    renderer.addNewUpload(file.path, uploadIndex);
     this.uploads.push(upload);
     this.uploadStatuses.push("uploading");
   }
@@ -537,7 +537,7 @@ class UploadFile {
           name: s3Upload.key,
           placeholder: false,
           size: s3Upload.file.size,
-          original_name: s3Upload.file.name
+          original_name: s3Upload.file.path
         } as UploadedFile;
       });

can hack the output, but will not pass yarn lint and only works for s3.

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