Installation issues

[vstadnytskyi]

I would appriciate if someone can help me isntalling it. My in-home developed microfluidic device doesn't behave as expected and I hoped to figure out why using the tool you developed. However, I am getting stuck with isntallation on my Mac Mojave computer. I have followed the installtion instructions (https://github.com/manifold-lang/pymanifold) and completed the first step. However, I cannot find where the docker put the image, hence, I cannot proceed to the next step. The root folder for the docker doesn't exist. (see below)

user:bin user-13$ docker info
...
Docker Root Dir: /var/lib/docker
...
user:/ user-13$ cd var/lib/docker
-bash: cd: var/lib/docker: No such file or directory

I also tried to instal dRea4l solver but got stuck as well.

user:dreal4 user-13$ bazel build //... --apple_generate_dsym
ERROR: /private/var/tmp/_bazel_femto-13/9101c4b47559e9f49ae7e434f8129424/external/local_config_cc/BUILD:62:5: in apple_cc_toolchain rule @local_config_cc//:cc-compiler-darwin_x86_64: Xcode version must be specified to use an Apple CROSSTOOL. If your Xcode version has changed recently, verify that "xcode-select -p" is correct and then try: "bazel shutdown" to re-run Xcode configuration
ERROR: Analysis of target '//dreal/api:api_test' failed; build aborted: Analysis of target '@local_config_cc//:cc-compiler-darwin_x86_64' failed; build aborted
INFO: Elapsed time: 0.177s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (0 packages loaded, 0 targets configured)

I have asked part of this question on Stackoverflow as well https://stackoverflow.com/questions/57134462/the-location-where-are-docker-images-stored-on-the-host-machine-doesnt-exist

[vstadnytskyi]

I have made some progress. I have figured how to install dReal4. However, the 'Variables' seems to be missing from dReal4.

femto13:microfluidics femto-13$ ipython3
Python 3.7.0 (v3.7.0:1bf9cc5093, Jun 26 2018, 23:26:24)

Type 'copyright', 'credits' or 'license' for more information
IPython 7.0.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import pymanifold
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-2bb352dc2fb6> in <module>
----> 1 import pymanifold

/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pymanifold/__init__.py in <module>
----> 1 from pymanifold.pymanifold import Schematic

/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pymanifold/pymanifold.py in <module>
      7 #  from build.lib.data.dreal.symbolic import Variable, logical_and, sin, cos
      8 #  from build.lib.data.dreal.api import CheckSatisfiability, Minimize
----> 9 from dreal.symbolic import Variable, logical_and, sin, cos
     10 from dreal.api import CheckSatisfiability, Minimize
     11 #  from pysmt.typing import REAL

ImportError: cannot import name 'Variable' from 'dreal.symbolic' (unknown location)

[jsreid13]

Hey @vstadnytskyi ! As long as you have pulled the docker image you should be able to run pyManifold without needing to install dReal4 as it is inside the docker image.

I believe the confusion is around what i meant by root folder, for that I mean the root for of this repository. So in order to run the tests, you need to first clone this repository with git clone https://github.com/manifold-lang/pymanifold.git on your computer, then navigate to the pymanifold folder that is created and run the command docker container run -it --rm -v $(pwd):/tmp -v $(pwd)/src:/tmp/src -w /tmp -e PYTHONPATH=/tmp jsreid13/pymanifold python3 tests/t_junction_test.py

In order to model your system, you can create your own script similar to t_junction_test.py that uses the dimensions of your system. If you have any other questions feel free to ask, I understand the documentation for this is limited so I'll try to help out however I can!

[vstadnytskyi]

The import of Variable works if it is done directly from dreal

see my question here. dreal/dreal4#145

In [7]: from dreal import Variable

In [8]: Variable.__dict__
Out[8]:
mappingproxy({'__init__': <instancemethod __init__ at 0x1119faeb8>,
              '__doc__': None,
              '__module__': 'dreal._dreal_py',

              'get_id': <instancemethod get_id at 0x1119faee8>,
              'get_type': <instancemethod get_type at 0x1119faf48>,
              '__str__': <instancemethod __str__ at 0x1119fafa8>,
              '__repr__': <instancemethod __repr__ at 0x1119f7048>,
              '__hash__': <instancemethod __hash__ at 0x1119f70a8>,
              '__add__': <instancemethod __add__ at 0x1119f7138>,
              '__radd__': <instancemethod __radd__ at 0x1119f7168>,
              '__sub__': <instancemethod __sub__ at 0x1119f71f8>,
              '__rsub__': <instancemethod __rsub__ at 0x1119f7228>,
              '__mul__': <instancemethod __mul__ at 0x1119f72b8>,
              '__rmul__': <instancemethod __rmul__ at 0x1119f72e8>,
              '__truediv__': <instancemethod __truediv__ at 0x1119f7378>,
              '__rtruediv__': <instancemethod __rtruediv__ at 0x1119f73a8>,
              '__pow__': <instancemethod __pow__ at 0x1119f7408>,
              '__pos__': <instancemethod __pos__ at 0x1119f7468>,
              '__neg__': <instancemethod __neg__ at 0x1119f74c8>,
              '__lt__': <instancemethod __lt__ at 0x1119f7528>,
              '__le__': <instancemethod __le__ at 0x1119f7588>,
              '__gt__': <instancemethod __gt__ at 0x1119f75e8>,
              '__ge__': <instancemethod __ge__ at 0x1119f7648>,
              '__eq__': <instancemethod __eq__ at 0x1119f76a8>,
              '__ne__': <instancemethod __ne__ at 0x1119f7708>,
              'Type': dreal._dreal_py.Variable.Type,
              'Real': Type.Real,
              'Int': Type.Int,
              'Bool': Type.Bool,
              'Binary': Type.Binary})

[vstadnytskyi]

Hey @vstadnytskyi ! As long as you have pulled the docker image you should be able to run pyManifold without needing to install dReal4 as it is inside the docker image.

I believe the confusion is around what i meant by root folder, for that I mean the root for of this repository. So in order to run the tests, you need to first clone this repository with git clone https://github.com/manifold-lang/pymanifold.git on your computer, then navigate to the pymanifold folder that is created and run the command docker container run -it --rm -v $(pwd):/tmp -v $(pwd)/src:/tmp/src -w /tmp -e PYTHONPATH=/tmp jsreid13/pymanifold python3 tests/t_junction_test.py

In order to model your system, you can create your own script similar to t_junction_test.py that uses the dimensions of your system. If you have any other questions feel free to ask, I understand the documentation for this is limited so I'll try to help out however I can!

It worked after I cloned it.
Valentyns-MacBook-Pro:pymanifold femto-13$ docker container run -it --rm -v $(pwd):/tmp -v $(pwd)/src:/tmp/src -w /tmp -e PYTHONPATH=/tmp jsreid13/pymanifold python3 tests/t_junction_test.py

But I know I want to import pymanifold into my script and build something else using this library.

I got it running but I have no idea how to customize the code to fit my design. Also, I was planning to use this package to simulate nano-droplet generation. Is it possible or does it just take care of laminar flow of fluids in capilaries? Has this code been used and described in any papers?

[jsreid13]

It has not been tested for nano-droplet generation, but I have tested it in collaboration with the droplet generation performed in this work https://www.mdpi.com/2072-666X/9/5/215 . It handles the laminar flow of fluids for droplet generation as outlined in the equations from this paper https://pubs.rsc.org/en/content/articlelanding/2010/LC/c002625e . This project was created for my Master's thesis which will be published in a couple weeks which will describe the code for this simulation.

[vstadnytskyi]

@jsreid13 Looking forward to read your thesis!