openworm/c302

The c302 framework for generating multiscale network models of C. elegans

About OpenWorm

OpenWorm aims to build the first comprehensive computational model of Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well-studied in biology, a deep, principled understanding of the biology of this organism remains elusive.

We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so, we are incorporating the data available from the scientific community into software models. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps.

You can earn a badge with us simply by trying out this package! Click on the image below to get started.

Quickstart

We have put together a Docker container that pulls together the major components of our simulation and runs it on your machine. When you get it all running it does the following:

1. Run our nervous system model, known as c302, on your computer.
2. In parallel, run our 3D worm body model, known as Sibernetic, on your computer, using the output of the nervous system model.
3. Produce graphs from the nervous system and body model that demonstrate its behavior on your computer for you to inspect.
4. Produce a movie showing the output of the body model.

Example Output

NOTE: Running the simulation for the full amount of time would produce content like the above. However, in order to run in a reasonable amount of time, the default run time for the simulation is limited. As such, you will see only a partial output, equivalent to about 5% of run time, compared to the examples above. To extend the run time, use the -d argument as described below.

Installation

Pre-requisites:

1. You should have at least 60 GB of free space on your machine and at least 2GB of RAM
2. You should be able to clone git repositories on your machine. Install git, or this GUI may be useful.

To Install:

1. Install Docker on your system.
2. If your system does not have enough free space, you can use an external hard disk. On MacOS X, the location for image storage can be specified in the Advanced Tab in Preferences. See this thread in addition for Linux instructions.

Running

1. Ensure the Docker daemon is running in the background (on MacOS/Windows there should be an icon with the Docker whale logo showing in the menu bar/system tray).
2. Open a terminal and run: git clone http://github.com/openworm/openworm; cd openworm
3. Optional: Run ./build.sh (or build.cmd on Windows). If you skip this step, it will download the latest released Docker image from the OpenWorm Docker hub.
4. Run ./run.sh (or run.cmd on Windows).
5. About 5-10 minutes of output will display on the screen as the steps run.
6. The simulation will end. Run stop.sh (stop.cmd on Windows) on your system to clean up the running container.
7. Inspect the output in the output directory on your local machine.

Advanced

Arguments

• -d [num] : Use to modify the duration of the simulation in milliseconds. Default is 15. Use 5000 to run for time to make the full movie above (i.e. 5 seconds).

Other things to try

• Open a terminal and run ./run-shell-only.sh (or run-shell-only.cmd on Windows). This will let you log into the container before it has run master_openworm.py. From here you can inspect the internals of the various checked out code bases and installed systems and modify things. Afterwards you'll still need to run ./stop.sh to clean up.
• If you wish to modify what gets installed, you should modify Dockerfile. If you want to modify what runs, you should modify master_openworm.py. Either way you will need to run build.sh in order to rebuild the image locally. Afterwards you can run normally.

FAQ

What is the Docker container?

The Docker container is a self-contained environment in which you can run OpenWorm simulations. It's fully set up to get you started by following the steps above. At the moment, it runs simulations and produces visualizations for you, but these visualizations must be viewed outside of the Docker container. While you do not need to know much about Docker to use OpenWorm, if you are planning on working extensively with the platform, you may benefit from understanding some basics. Docker Curriculum is an excellent tutorial for beginners that is straightforward to work through (Sections 1 - 2.5 are plenty sufficient).

Is it possible to modify the simulation without having to run build.sh?

Yes, but it is marginally more complex. The easiest way is to modify anything in the Docker container once you are inside of it - it will work just like a bash shell. If you want to modify any code in the container, you'll need to use an editor that runs in the terminal, like nano. Once you've modified something in the container, you don't need to re-build. However, if you run stop.sh once you exit, those changes will be gone.

How do I access more data than what is already output?

The simulation by default outputs only a few figures and movies to your home system (that is, outside of the Docker container). If you want to access the entire output of the simulation, you will need to copy it from the Docker container.

For example, say you want to extract the worm motion data. This is contained in the file worm_motion_log.txt, which is found in the /home/ow/sibernetic/simulations/[SPECIFIC_TIMESTAMPED_DIRECTORY]/worm_motion_log.txt. The directory [SPECIFIC_TIMESTAMPED_DIRECTORY] will have a name like C2_FW_2018_02-12_18-36-32, and its name can be found by checking the output directory. This is actually the main output directory for the simulation, and contains all output, including cell modelling and worm movement.

Once the simulation ends and you exit the container with exit, but before you run stop.sh, run the following command from the openworm-docker-master folder:

docker cp openworm:/home/ow/sibernetic/simulations/[SPECIFIC_TIMESTAMPED_DIRECTORY]/worm_motion_log.txt ./worm_motion_log.txt

This will copy the file from the Docker container, whose default name is openworm. It is crucial that you do not run stop.sh before trying to get your data out (see below)

What is the difference between exit and stop.sh?

When you are in the Docker Container openworm, and are done interacting with it, you type exit to return to your system's shell. This stops execution of anything in the container, and that container's status is now Exited. If you try to re-start the process using run-shell-only.sh, you will get an error saying that the container already exists. You can choose, at this point, to run stop.sh. Doing so will remove the container and any files associated with it, allowing you to run a new simulation. However, if you don't want to remove that container, you will instead want to re-enter it.

How do I enter a container I just exited?

If you run stop.sh you'll delete your data and reset the container for a new run. If, however, you don't want to do that, you can re-enter the Docker container like this:

docker start openworm                 # Restarts the container
docker exec -it openworm /bin/bash    # Runs bash inside the container

This tells Docker to start the container, to execute commands (exec) with an interactive, tty (-it) bash (bash) shell in the container openworm.

You'll be able to interact with the container as before.

Documentation

to find out more about OpenWorm, please see the documentation at http://docs.openworm.org or join us on Slack.

This repository also contains project-wide tracking via high-level issues and milestones.

c302's Issues

Update documentation and code to run c302/c302_*.py as python -m c302.c302_*

Relative imports break in possibly unexpected ways when you run a script from inside of its package directory rather than let python do it for you with -m

owmeta installation fails on GH actions

@mwatts15 Could you have a quick look at the installation of owmeta as used in the CI test here: https://github.com/openworm/c302/blob/development/.github/workflows/non_omv.yml#L23?

It fails: https://github.com/openworm/c302/runs/4035587014?check_suite_focus=true with an error:

owmeta_core.bundle.exceptions.BundleNotFound: Missing bundle "openworm/owmeta-data" at version 6: Bundle directory, "/home/runner/.owmeta/bundles/openworm%2Fowmeta-data/6", does not exist for the specified version

but the dir /home/runner/.owmeta/bundles/openworm%2Fowmeta-data/1 does exist

Update OpenWormReader to use the latest version of owmeta (pt 2)

Should accept a DataWithEvidenceDataSource identifier for the source of
neuron network and muscle data, etc.

blocked by #12

Add WormNeuroAtlas to dependencies and add to tests

Add to https://github.com/openworm/c302/blob/master/setup.py

Add a new test after OpenWormReader to https://github.com/openworm/c302/blob/master/.github/workflows/non_omv.yml

Document lfs checkout from this repo

Many image files in this repo are stored using git lfs, needs to be something in the README about this...

Remove assumptions of spreadsheet reader being used

In method names in particular, but possibly subtler distinctions as well.

Add generated activity images to this repo

Move tests to travis-ci.com

Need to move tests on this from travis-ci.org to travis-ci.com. They will eventually move to github actions, but as a short term solution (since travis-ci.org will shut on June 15th) tests can be moved to travis-ci.com.

This seems to be set up in Settings, but there is a block on this under Third Party Access

@mwatts15 It has you down as requesting this. Any reason not to grant access to this?

Porting the computation of C302 neural network operations to my neural morphology chip.

Hello, respected developer. I have two questions. The first one is that I want to transplant the neural network computation of C302 to my neural morphology chip. However, currently my neural morphology chip only supports C language, so how can I use C language to reconstruct the network structure of C302 and perform computation on my chip.
Secondly, I am currently well aware that the definition of network structure and neural network calculations that rely on stimulating cells all come from LEMS files, such as LEMS_c302_A_Full.xml. But when I was reading the LEMS file, I found that I couldn't find the three files described in the following code in the local environment, so I would like to ask where these three files are located.

    <Include file="Cells.xml" />
    <Include file="Networks.xml" />
    <Include file="Simulation.xml" />

Add all omv tests from original repo

List and dictionary command line arguments from README not executable in some shells

This command in the README:
c302 MyNetwork parameters_C -cells ["AVBR","VD3"] -cellstostimulate ["AVBR"] -paramoverride {"unphysiological_offset_current":"2.9pA"} -duration 300

Does not execute as-is in some shells, like ZSH, which attempt to parse ["AVBR","VD3"] as a shell glob and fail. (For ZSH, the failure produces a message, zsh: no matches found: [AVBR,VD3], rather than removing quote marks and passing [AVBR,VD3] to c302 as Bash apparently does.) ["AVBR"] is handled similarly. On the other hand, {"unphysiological_offset_current":"2.9pA"} apparently isn't interpreted as a glob and is handled as intended.

Use this as default for sibernetic

No module named 'bioparameters'

I installed c302, following the instructions. When running to create a new network. I entered the following command.

c302 MyNetwork parameters_C -cells ["AVBR","VD3"] -cellstostimulate ["AVBR"] -paramoverride {"unphysiological_offset_current":"2.9pA"} -duration 300

Use OpenWorm backers data source to get backers for c302 network generation.

Depends on openworm/owmeta#467

Create a c302 DataTranslator and DataSources

PyOpenWorm has a notion of DataTranslators that describe how data get from
one form to another and each of those forms is called a DataSource. A
DataSource should be created to describe the input to c302 and a DataSource
should be created to describe the output NeuroML files. The DataTranslator
should have a translate method which runs c302 with the first DataSource
type and outputs the second. The first DataSource should have a Translation
linking it back to the PyOpenWorm insert_worm DataSource (TBD:
openworm/owmeta#364).

blocked by openworm/owmeta#364

Make a proper unit test suite

There's a test.sh script (which also doesn't work with the python 3
updates) that does not have clear pass/fail which is unhelpful for quickly
diagnosing errors.

runnin sh test.sh in cmd

Hello
now i am trying to simulate the c302 neurons of the worm.

so i have done :

git clone https://github.com/openworm/c302.git
cd c302
python setup.py install

sh test.sh

and i got the error in attachment
can you please give me advice

Compare running times of NeuroML file generation with OpenWormReader vs Spreadsheet reader

OpenWormReader will undoubtedly take longer. Must determine whether the
difference is substatial enough to merit doing query of the PyOW database
at a different phase (i.e., with a pow translate). This had been a
limiting factor to inclusion in c302/CElegansNeuroML previously.

blocked by #10

Can't connect to PyOpenWorm

I called the command

c302 -h

And found this error

FileNotFoundError: [Errno 2] No such file or directory: '/Users/username/PyOpenWorm/.pow/worm.db.lock' Failed to open the data source because: Could not open the database file "/Users/username/PyOpenWorm/.pow/worm.db"
c302 >>> Can't connect to PyOpenWorm: ...
PyOpenWorm connection failed: Could not open the database file "/Users/username/PyOpenWorm/.pow/worm.db". Perhaps you need to do a "pow clone"?

It seems like c302 cannot connect to PyOpenWorm. Where can I access this database?

Data c302

Data Provenance

Hello everyone!

I think it would be useful to made a readme.txt in the data folders to account about the data provenance.

Anyway, could anyone tell me where is the data coming from:

I am using neuroML2 models of neurons, herm_full_edgelist_MODIFIED, and CElegansNeuronTables.csv.

Thanks!

Clarify pipeline from ChannelWorm to c302

openworm/ChannelWorm2#12

first installation error : unable to download c302 module

Hello,
I tried to use sibernetic_c302.py to simulate C. eleganse,
but error occurred.

Collecting c302
  Using cached c302-0.7.0.tar.gz (35.1 MB)
Requirement already satisfied: numpy in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from c302) (1.19.4)
Requirement already satisfied: xlrd in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from c302) (2.0.1)
Collecting xlwt
  Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Requirement already satisfied: libNeuroML>=0.2.39 in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from c302) (0.2.53)
Requirement already satisfied: pyNeuroML>=0.3.11 in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from c302) (0.5.5)
Collecting pyopenworm==0.7.1
  Using cached PyOpenWorm-0.7.1.tar.gz (339 kB)
Requirement already satisfied: lxml in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from libNeuroML>=0.2.39->c302) (4.6.2)
Requirement already satisfied: six in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from libNeuroML>=0.2.39->c302) (1.15.0)
Requirement already satisfied: argparse in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from pyNeuroML>=0.3.11->c302) (1.4.0)
Requirement already satisfied: pylems>=0.4.9.1 in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from pyNeuroML>=0.3.11->c302) (0.5.1)
Requirement already satisfied: airspeed==0.5.4dev-20150515 in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from pyNeuroML>=0.3.11->c302) (0.5.4.dev20150515)
Requirement already satisfied: neuromllite>=0.1.9 in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from pyNeuroML>=0.3.11->c302) (0.1.9)
Requirement already satisfied: kiwisolver<=1.1.0 in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from pyNeuroML>=0.3.11->c302) (1.1.0)
Requirement already satisfied: matplotlib in c:\users\user\appdata\local\programs\python\python39\lib\site-packages (from pyNeuroML>=0.3.11->c302) (3.3.3)
Collecting bibtexparser==0.6.1
  Using cached bibtexparser-0.6.1.tar.gz (26 kB)
Collecting BTrees==4.0.8
  Using cached BTrees-4.0.8.tar.gz (608 kB)

DEPRECATION: The -b/--build/--build-dir/--build-directory option is deprecated. pip 20.3 will remove support for this functionality. A possible replacement is use the TMPDIR/TEMP/TMP environment variable, possibly combined with --no-clean. You can find discussion regarding this at https://github.com/pypa/pip/issues/8333.
    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\USER\AppData\Local\Programs\Python\Python39\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\USER\\AppData\\Local\\Temp\\pycharm-packaging\\btrees\\setup.py'"'"'; __file__='"'"'C:\\Users\\USER\\AppData\\Local\\Temp\\pycharm-packaging\\btrees\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\USER\AppData\Local\Temp\pip-pip-egg-info-kckznqqe'
         cwd: C:\Users\USER\AppData\Local\Temp\pycharm-packaging\btrees\
    Complete output (46 lines):
    WARNING: The wheel package is not available.
      ERROR: Command errored out with exit status 1:
       command: 'C:\Users\USER\AppData\Local\Programs\Python\Python39\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\USER\\AppData\\Local\\Temp\\pip-wheel-rczjvzy3\\persistent\\setup.py'"'"'; __file__='"'"'C:\\Users\\USER\\AppData\\Local\\Temp\\pip-wheel-rczjvzy3\\persistent\\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 'C:\Users\USER\AppData\Local\Temp\pip-wheel-h6lc6nk8'
           cwd: C:\Users\USER\AppData\Local\Temp\pip-wheel-rczjvzy3\persistent\
      Complete output (8 lines):
      WARNING: The wheel package is not available.
      WARNING: The wheel package is not available.
      usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
         or: setup.py --help [cmd1 cmd2 ...]
         or: setup.py --help-commands
         or: setup.py cmd --help
    
      error: invalid command 'bdist_wheel'
      ----------------------------------------
      ERROR: Failed building wheel for persistent
    ERROR: Failed to build one or more wheels
    Traceback (most recent call last):
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\installer.py", line 126, in fetch_build_egg
        subprocess.check_call(cmd)
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\subprocess.py", line 373, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python39\\python.exe', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', 'C:\\Users\\USER\\AppData\\Local\\Temp\\tmpuvxibmva', '--quiet', 'persistent']' returned non-zero exit status 1.
    
    The above exception was the direct cause of the following exception:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\USER\AppData\Local\Temp\pycharm-packaging\btrees\setup.py", line 116, in <module>
        setup(name='BTrees',
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\__init__.py", line 152, in setup
        _install_setup_requires(attrs)
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\__init__.py", line 147, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\dist.py", line 673, in fetch_build_eggs
        resolved_dists = pkg_resources.working_set.resolve(
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\pkg_resources\__init__.py", line 764, in resolve
        dist = best[req.key] = env.best_match(
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\pkg_resources\__init__.py", line 1049, in best_match
        return self.obtain(req, installer)
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\pkg_resources\__init__.py", line 1061, in obtain
        return installer(requirement)
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\dist.py", line 732, in fetch_build_egg
        return fetch_build_egg(self, req)
      File "C:\Users\USER\AppData\Local\Programs\Python\Python39\lib\site-packages\setuptools\installer.py", line 128, in fetch_build_egg
        raise DistutilsError(str(e)) from e
    distutils.errors.DistutilsError: Command '['C:\\Users\\USER\\AppData\\Local\\Programs\\Python\\Python39\\python.exe', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', 'C:\\Users\\USER\\AppData\\Local\\Temp\\tmpuvxibmva', '--quiet', 'persistent']' returned non-zero exit status 1.

I thought it's maybe the problem of the latest version,
so I tried to download 0.6.0 version of c302

Collecting c302==0.6.0
  Using cached c302-0.6.0.tar.gz (642 kB)

DEPRECATION: The -b/--build/--build-dir/--build-directory option is deprecated. pip 20.3 will remove support for this functionality. A possible replacement is use the TMPDIR/TEMP/TMP environment variable, possibly combined with --no-clean. You can find discussion regarding this at https://github.com/pypa/pip/issues/8333.
    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\USER\AppData\Local\Programs\Python\Python39\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\USER\\AppData\\Local\\Temp\\pycharm-packaging\\c302\\setup.py'"'"'; __file__='"'"'C:\\Users\\USER\\AppData\\Local\\Temp\\pycharm-packaging\\c302\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\USER\AppData\Local\Temp\pip-pip-egg-info-evn57mh0'
         cwd: C:\Users\USER\AppData\Local\Temp\pycharm-packaging\c302\
    Complete output (8 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\USER\AppData\Local\Temp\pycharm-packaging\c302\setup.py", line 6, in <module>
        import c302
      File "C:\Users\USER\AppData\Local\Temp\pycharm-packaging\c302\c302\__init__.py", line 1416
        print 555522
              ^
    SyntaxError: Missing parentheses in call to 'print'. Did you mean print(555522)?
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
WARNING: You are using pip version 20.2.3; however, version 20.3.3 is available.
You should consider upgrading via the 'C:\Users\USER\AppData\Local\Programs\Python\Python39\python.exe -m pip install --upgrade pip' command.

But an even weirder error occurred.
Please help...

Deprecated dependencies: Use command line interface to create new network

This is for the Readme, in Usage Examples: Section 2) Use command line interface to create new network
Specifically, for this command line example code:

c302 MyNetwork parameters_C -cells ["AVBR","VD3"] -cellstostimulate ["AVBR"] -paramoverride {"unphysiological_offset_current":"2.9pA"} -duration 300

There's a lot of things going on here. I had some issue with owmeta that I dont recall what they were.

The wrapt package that was setup on my system, I guess when I installed this, was too new. I had to downgrade to version 1.11.1.

Now I'm getting this:
ImportError: cannot import name inspect.formatargspec. I guess the code, or one of its dependencies, is trying to use the formatargspec function from the inspect module, which has been deprecated and removed in Python 3.11. I'm reading that the inspect.signature function replaced it.

If I try to correct that code on my system, I think I will get sucked into a rabbit hole because I do not know the design of this software.

Reason I want to use this functionality
I was wanting to do a variation on that command in order to generate the LEMS files, and I guess the NeuroML 2 files, for each neuron for a script that:

1. Iterates over a range of current clamp values.
2. Runs a simulation for each value.
3. Records the neuron's response.
4. Identifies the minimum active response and the maximum sustainable response.
5. Saves a record of the test results to have the input current value, the output current value, and the ISI if there is one.

These tests would be ran on one neuron each. Not to simulate the interactions between the neurons.

Is there another way I can generate that LEMS file, such as another program, or the possibility of running that command from the openworm docker image?

I don't know how to run the command from the openworm docker image, if doing that is possible. But I can figure it out if the other stuff I am trying does not work. Right now I am setting up older versions of linux in virtual machines trying to find one that is not too old to prevent me from installing this program in it, while not being too new to run that command.

Pass in reader objects rather than names of readers for for data_reader arguments

Allows to configure readers in any way that's needed prior to use (e.g.,
the spreadsheet location, PyOW context). There doesn't seem to be any
reason that users of the data reader either need to initialize or resolve
the readers differently for a given name, so it's better not to expect them
to.

fatal error: 'H5public.h' file not found

After cloning the c302 repo and running pip3 install . I am getting the following error-

/var/folders/b6/75cxrjwd3vb2ljjm8mxm452h0000gn/T/H5closeoesewhwn.c:1:10: fatal error: 'H5public.h' file not found

Replace unqualified relative imports with explicit relative imports

In Python 3, such imports do not work any longer.

Explicit relative import:

from . import bioparameters

Update OpenWormReader to use the latest version of PyOpenWorm (pt 1)

As a first approximation, can just hard-code
<http://openworm.org/entities/bio#worm0>
as the context to query against (it's sort of the 'top-level' context
produced by insert_worm.py into the OpenWormData repo). Will be modified in
owupd1 to its final form.

Quick test problem

hello
I am try to install c302 according to README.md

I have done:
git clone https://github.com/openworm/c302.git
cd c302
python setup.py install

when I try to run

owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'

I met up with the problem of

so I turned to run

~/opt/anaconda3/bin/owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'

and succeed with

but afterwards, when I try to run the quick test

python c302/c302_Pharyngeal.py

I get the error of:

(The ! mark is because I added something to the dataobject.py file like this:

)

can you please give me advice to overcome this?
Thanks a lot