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SchmollerLab / Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
BSD 3-Clause "New" or "Revised" License
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Installing javabridge - did not complete #382

Closed makotojohira closed 9 months ago

makotojohira commented 1 year ago

Description:

I have installed acdc via Anaconda onto my MacBook Air with MacOS v 13.5. The Welcome page opened and when I tried the Wizard button, the Installing javabridge window opened, a circling icon appeared, but the installation did not appear to complete (there was no dialog or popup indicating installation was complete). I tried the Wizard button again, and the installing javabridge window popped open again. I tried this several times before reporting the installation failure here. Thank you.

Way to reproduce:

No response

(Optional) Link to data to reproduce error:

No response

Terminal output:

No response

Version information:

No response

ElpadoCan commented 1 year ago

Hi @makotojohira, I'm sorry to hear you are having these issues. Do you have a Apple Silicon Mac (M1 or M2) or a Intel based Mac?

Unfortunately, as far as I know, javabridge doesn't work on mac M1 or M2 and I don't think the developer will ever fix it.

We are working on an alternative but it's going to take some time. In the meantime, you will have to create the data structure manually or with a Fiji macro.

If you are familiar with the ImageJ macro language, we already have two macros on our GitHub page [here] (https://github.com/SchmollerLab/Cell_ACDC/tree/main/FijiMacros) that would create the data structure starting from the microscopy file.

The other option is that you convert the files to Tif and then I can add a small utility to rearrange the files into the required data structure.

Let me know what you prefer to do, thanks!

Cheers Francesco

makotojohira commented 1 year ago

Hi Francesco,

Thanks for your quick reply. I am using an Intel based Mac. And thank you for the link to the Fiji macros. My image is already a .tif file. Should I use your macro on my .tif images?

Thanks again,

Makoto Ohira Rhind Lab https://www.umassmed.edu/rhindlab/ Department of Biochemistry and Molecular Biotechnology University of Massachusetts Chan Medical School LRB 940D 364 Plantation Street Worcester, MA 01655

From: Francesco Padovani @.> Sent: Sunday, July 30, 2023 12:37 PM To: SchmollerLab/Cell_ACDC @.> Cc: Ohira, Makoto @.>; Mention @.> Subject: Re: [SchmollerLab/Cell_ACDC] Installing javabridge - did not complete (Issue #382)

Hi @makotojohirahttps://github.com/makotojohira, I'm sorry to hear you are having these issues. Do you have a Apple Silicon Mac (M1 or M2) or a Intel based Mac?

Unfortunately, as far as I know, javabridge doesn't work on mac M1 or M2 and I don't think the developer will ever fix it.

We are working on an alternative but it's going to take some time. In the meantime, you will have to create the data structure manually or with a Fiji macro.

If you are familiar with the ImageJ macro language, we already have two macros on our GitHub page [here] (https://github.com/SchmollerLab/Cell_ACDC/tree/main/FijiMacros) that would create the data structure starting from the microscopy file.

The other option is that you convert the files to Tif and then I can add a small utility to rearrange the files into the required data structure.

Let me know what you prefer to do, thanks!

Cheers Francesco

— Reply to this email directly, view it on GitHubhttps://github.com/SchmollerLab/Cell_ACDC/issues/382#issuecomment-1657215839, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWW7OFF2ALD556BGKNSIHCTXS2EVJANCNFSM6AAAAAA25FRP2M. You are receiving this because you were mentioned.Message ID: @.***>

ElpadoCan commented 1 year ago

Ok if it's tif you don't need javabridge nor the Fiji macros since they are both for opening raw microscopy files and convert them into tif.

However, we still need to create the data structure required by acdc.

How many dimensions do you have in your tif file? Are they 2D over time? Or z-stacks? Or z-stacks over time? How many tif files do you end up having in a typical experiment?

The data structure required is a single tif file per channel. The tif file can be a single 2D, 3D (z-stack or 2D over time), or 4D (3D z-stacks over time). Then you can have multiple positions per experiment. A typical scenario is to start from a single cell (each cell is a position) and image over time (the cell grows and divide generating a colony).

Anyway, as soon as I know how you have the tif files arranged we easily rearrange them into acdc structure.

If you think it can help, you can also share a sample of the dataset on Google drive and share it to my email padovaf@tcd.ie

Let me know thanks!

Cheers Francesco

makotojohira commented 1 year ago

Hi Francesco,

When I open acdc, I have two windows open. One is Welcome window, the other is Cell-ACDC window.

In the Welcome window, when I click on Launch Wizard, it automatically opens the Installing javabridge window and when I click OK, it stalls with the rotating rainbow circle and never installs the program.

When I click on Test segmentation with my image/video, it opens Cell-ACDC - GUI, and if I click on the page + button, the Load image file button (after putting the .tif file in a folder called Image), it ultimately gives me a critical error window, and tells me to restart ACDC.

I do not have z-stacks or time-lapse image series - but a lab mate who will ultimately use acdc has those images. I am just trying to install and test the acdc program.

With a single, simple 1-channel .tif image that I would like to upload and run a test segmentation on, just to demonstrate to myself that I have everything I need for my lab mates to use acdc, how can I get past these error messages?

Many thanks!

Makoto

Makoto Ohira Rhind Lab https://www.umassmed.edu/rhindlab/ Department of Biochemistry and Molecular Biotechnology University of Massachusetts Chan Medical School LRB 940D 364 Plantation Street Worcester, MA 01655

From: Francesco Padovani @.> Sent: Sunday, July 30, 2023 1:17 PM To: SchmollerLab/Cell_ACDC @.> Cc: Ohira, Makoto @.>; Mention @.> Subject: Re: [SchmollerLab/Cell_ACDC] Installing javabridge - did not complete (Issue #382)

Ok if it's tif you don't need javabridge nor the Fiji macros since they are both for opening raw microscopy files and convert them into tif.

However, we still need to create the data structure required by acdc.

How many dimensions do you have in your tif file? Are they 2D over time? Or z-stacks? Or z-stacks over time? How many tif files do you end up having in a typical experiment?

The data structure required is a single tif file per channel. The tif file can be a single 2D, 3D (z-stack or 2D over time), or 4D (3D z-stacks over time). Then you can have multiple positions per experiment. A typical scenario is to start from a single cell (each cell is a position) and image over time (the cell grows and divide generating a colony).

Anyway, as soon as I know how you have the tif files arranged we easily rearrange them into acdc structure.

If you think it can help, you can also share a sample of the dataset on Google drive and share it to my email @.**@.>

Let me know thanks!

Cheers Francesco

— Reply to this email directly, view it on GitHubhttps://github.com/SchmollerLab/Cell_ACDC/issues/382#issuecomment-1657223602, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWW7OFBCFCF3AZVKMC2VLHLXS2JJHANCNFSM6AAAAAA25FRP2M. You are receiving this because you were mentioned.Message ID: @.***>

ElpadoCan commented 1 year ago

Ok great, then I need the error messages you get. You can either send me the log files or copy paste from the terminal.

One thing that I can say is that the tif file(s) should be in a folder called Images and not Image.

For the javabridge installation instead in principle it should work on an Intel mac but I don't have one (I have only a M1 Mac) myself. I can send you detailed instructions if you want to give it a try.

However, while you are just testing out, if I was you, I would not try to install javabridge since it's needed only to open raw microscopy files and covert them to tif (and you already have tif files).

We are trying to migrate away from javabridge anyway because it's a pain to install and there seems to be better options now.

Cheers Francesco

makotojohira commented 1 year ago

OK thanks again Francesco. I have copied the following error messages from Terminal:

##############

WARNING: Cell-ACDC is in error state. Please, restart.

====================================

Closing GUI logger...

Traceback (most recent call last):

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/connectionpool.py", line 714, in urlopen

httplib_response = self._make_request(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/connectionpool.py", line 403, in _make_request

self._validate_conn(conn)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1053, in _validate_conn

conn.connect()

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/connection.py", line 419, in connect

self.sock = ssl_wrap_socket(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket

ssl_sock = _ssl_wrap_socket_impl(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl

return ssl_context.wrap_socket(sock, server_hostname=server_hostname)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/ssl.py", line 501, in wrap_socket

return self.sslsocket_class._create(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/ssl.py", line 1041, in _create

self.do_handshake()

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/ssl.py", line 1310, in do_handshake

self._sslobj.do_handshake()

ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/requests/adapters.py", line 486, in send

resp = conn.urlopen(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/connectionpool.py", line 798, in urlopen

retries = retries.increment(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/urllib3/util/retry.py", line 592, in increment

raise MaxRetryError(_pool, url, error or ResponseError(cause))

urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='hmgubox2.helmholtz-muenchen.de', port=443): Max retries exceeded with url: /index.php/s/CaMdYXiwxxoq3Ts/download/TimeLapse_2D.zip (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)')))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/cellacdc/help/welcome.py", line 49, in run

self.exp_path = myutils.download_examples(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/cellacdc/myutils.py", line 855, in download_examples

download_url(

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/cellacdc/myutils.py", line 1161, in download_url

response = requests.get(url, stream=True, timeout=20)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/requests/api.py", line 73, in get

return request("get", url, params=params, **kwargs)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/requests/api.py", line 59, in request

return session.request(method=method, url=url, **kwargs)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/requests/sessions.py", line 589, in request

resp = self.send(prep, **send_kwargs)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/requests/sessions.py", line 703, in send

r = adapter.send(request, **kwargs)

File "/Users/makotoohira/miniconda3/envs/acdc/lib/python3.9/site-packages/requests/adapters.py", line 517, in send

raise SSLError(e, request=request)

requests.exceptions.SSLError: HTTPSConnectionPool(host='hmgubox2.helmholtz-muenchen.de', port=443): Max retries exceeded with url: /index.php/s/CaMdYXiwxxoq3Ts/download/TimeLapse_2D.zip (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)')))

zsh: abort acdc

(acdc) @.*** ~ %

##############

ElpadoCan commented 1 year ago

Oh jeez, that error happens because Cell-ACDC is trying to download the example data automatically, but it fails because the connection to our cloud times out. The reason is that the data is on our campus cloud (we are in Helmholtz Munich), but the Helmholtz centre was the victim of a massive hacker attack some months ago and many systems are still down.

I will think of a solution first thing tomorrow morning. In the meantime, you can download the timelapse example data from here and the z-stacks from here.

Note that if you need more test data we published the entire dataset that we used in the paper here.

Let me know if it works, thanks!

makotojohira commented 1 year ago

Fantastic - thank you so much!

Makoto Ohira Rhind Lab https://www.umassmed.edu/rhindlab/ Department of Biochemistry and Molecular Biotechnology University of Massachusetts Chan Medical School LRB 940D 364 Plantation Street Worcester, MA 01655

From: Francesco Padovani @.> Sent: Sunday, July 30, 2023 2:53 PM To: SchmollerLab/Cell_ACDC @.> Cc: Ohira, Makoto @.>; Mention @.> Subject: Re: [SchmollerLab/Cell_ACDC] Installing javabridge - did not complete (Issue #382)

Oh jeez, that error happens because Cell-ACDC is trying to download the example data automatically, but it fails because the connection to our cloud times out. The reason is that the data is on our campus cloud (we are in Helmholtz Munich), but the Helmholtz centre was the victim of a massive hacker attack some months ago and many systems are still down.

I will think of a solution first thing tomorrow morning. In the meantime, you can download the timelapse example data from here https://hmgubox2.helmholtz-muenchen.de/index.php/s/CaMdYXiwxxoq3Ts/download/TimeLapse_2D.zip and the z-stacks from herehttps://hmgubox2.helmholtz-muenchen.de/index.php/s/CXZDoQMANNrKL7a/download/Yeast_Analysed_multi3D_zStacks.zip.

Note that if you need more test data we published the entire dataset that we used in the paper herehttps://zenodo.org/record/6795124.

Let me know if it works, thanks!

— Reply to this email directly, view it on GitHubhttps://github.com/SchmollerLab/Cell_ACDC/issues/382#issuecomment-1657241354, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWW7OFGVNQG2ALLGJNNXR23XS2UTPANCNFSM6AAAAAA25FRP2M. You are receiving this because you were mentioned.Message ID: @.***>

makotojohira commented 1 year ago

Hi Francesco,

Since I was able to install acdc on my machine I asked my labmates to proceed. But they ran into issues, and we realized there were several differences between their laptops and mine.

While all use Apple Macbooks, mine has Intel chips, both labmates have M2 chips.

I am running MacOS 13.5, one is running v13.4 and one is running v12.4 (but will update to most recent before installing acdc).

We are not able to install Python 3.9, and can only install Python 3.11 (however, the installation completed for me despite that difference).

The person with MacOS v13.4 tried installing with Anaconda, and got the following error:

################

(base) @.*** ~ % conda activate acdc

(acdc) @.*** ~ % python -m pip install --upgrade pip

Requirement already satisfied: pip in ./anaconda3/envs/acdc/lib/python3.11/site-packages (23.2.1)

(acdc) @.*** ~ % pip install "cellacdc[gui]"

Collecting cellacdc[gui]

Obtaining dependency information for cellacdc[gui] from https://files.pythonhosted.org/packages/69/a4/d7cbaa2cdc5d520f7f6d71a2e6026527d5de1f691edd9ec3557ee77f9611/cellacdc-1.3.0-py3-none-any.whl.metadata

Using cached cellacdc-1.3.0-py3-none-any.whl.metadata (15 kB)

WARNING: cellacdc 1.3.0 does not provide the extra 'gui'

Collecting numpy (from cellacdc[gui])

Obtaining dependency information for numpy from https://files.pythonhosted.org/packages/86/a1/b8ef999c32f26a97b5f714887e21f96c12ae99a38583a0a96e65283ac0a1/numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata

Downloading numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB)

Collecting opencv-python-headless (from cellacdc[gui])

Obtaining dependency information for opencv-python-headless from https://files.pythonhosted.org/packages/9d/df/88bc1f767d880d4629d71d6d3907bf89aea4506b828e9ede7d3846a0912d/opencv_python_headless-4.8.0.74-cp37-abi3-macosx_11_0_arm64.whl.metadata

Using cached opencv_python_headless-4.8.0.74-cp37-abi3-macosx_11_0_arm64.whl.metadata (19 kB)

Collecting natsort (from cellacdc[gui])

Obtaining dependency information for natsort from https://files.pythonhosted.org/packages/ef/82/7a9d0550484a62c6da82858ee9419f3dd1ccc9aa1c26a1e43da3ecd20b0d/natsort-8.4.0-py3-none-any.whl.metadata

Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)

Collecting h5py (from cellacdc[gui])

Obtaining dependency information for h5py from https://files.pythonhosted.org/packages/37/82/859d9fc800a316e692bd040437d45613512b43d49fb0435c5bbab9e71511/h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata

Downloading h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.5 kB)

Collecting PyQt5>5.15 (from cellacdc[gui])

Using cached PyQt5-5.15.9.tar.gz (3.2 MB)

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... error

error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.

│ exit code: 1

╰─> [25 lines of output]

  Traceback (most recent call last):

    File "/Users/dishakhanna/anaconda3/envs/acdc/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>

      main()

    File "/Users/dishakhanna/anaconda3/envs/acdc/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main

      json_out['return_val'] = hook(**hook_input['kwargs'])

                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

    File "/Users/dishakhanna/anaconda3/envs/acdc/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel

      whl_basename = backend.build_wheel(metadata_directory, config_settings)

                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-build-env-ejqir_w8/overlay/lib/python3.11/site-packages/sipbuild/api.py", line 46, in build_wheel

      project = AbstractProject.bootstrap('wheel',

                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-build-env-ejqir_w8/overlay/lib/python3.11/site-packages/sipbuild/abstract_project.py", line 87, in bootstrap

      project.setup(pyproject, tool, tool_description)

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-build-env-ejqir_w8/overlay/lib/python3.11/site-packages/sipbuild/project.py", line 586, in setup

      self.apply_user_defaults(tool)

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-install-0selmavb/pyqt5_4c291cf1ddc944d0904228b8048fe8b1/project.py", line 68, in apply_user_defaults

      super().apply_user_defaults(tool)

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-build-env-ejqir_w8/overlay/lib/python3.11/site-packages/pyqtbuild/project.py", line 70, in apply_user_defaults

      super().apply_user_defaults(tool)

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-build-env-ejqir_w8/overlay/lib/python3.11/site-packages/sipbuild/project.py", line 237, in apply_user_defaults

      self.builder.apply_user_defaults(tool)

    File "/private/var/folders/py/8tyl67h159j6lw2s71x0ld9w0000gn/T/pip-build-env-ejqir_w8/overlay/lib/python3.11/site-packages/pyqtbuild/builder.py", line 69, in apply_user_defaults

      raise PyProjectOptionException('qmake',

  sipbuild.pyproject.PyProjectOptionException

  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: metadata-generation-failed

× Encountered error while generating package metadata.

╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.

hint: See above for details.

Makoto Ohira Rhind Lab https://www.umassmed.edu/rhindlab/ Department of Biochemistry and Molecular Biotechnology University of Massachusetts Chan Medical School LRB 940D 364 Plantation Street Worcester, MA 01655

From: Francesco Padovani @.> Sent: Sunday, July 30, 2023 2:53 PM To: SchmollerLab/Cell_ACDC @.> Cc: Ohira, Makoto @.>; Mention @.> Subject: Re: [SchmollerLab/Cell_ACDC] Installing javabridge - did not complete (Issue #382)

Oh jeez, that error happens because Cell-ACDC is trying to download the example data automatically, but it fails because the connection to our cloud times out. The reason is that the data is on our campus cloud (we are in Helmholtz Munich), but the Helmholtz centre was the victim of a massive hacker attack some months ago and many systems are still down.

I will think of a solution first thing tomorrow morning. In the meantime, you can download the timelapse example data from here https://hmgubox2.helmholtz-muenchen.de/index.php/s/CaMdYXiwxxoq3Ts/download/TimeLapse_2D.zip and the z-stacks from herehttps://hmgubox2.helmholtz-muenchen.de/index.php/s/CXZDoQMANNrKL7a/download/Yeast_Analysed_multi3D_zStacks.zip.

Note that if you need more test data we published the entire dataset that we used in the paper herehttps://zenodo.org/record/6795124.

Let me know if it works, thanks!

— Reply to this email directly, view it on GitHubhttps://github.com/SchmollerLab/Cell_ACDC/issues/382#issuecomment-1657241354, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWW7OFGVNQG2ALLGJNNXR23XS2UTPANCNFSM6AAAAAA25FRP2M. You are receiving this because you were mentioned.Message ID: @.***>

ElpadoCan commented 1 year ago

Hi Makoto,

I just released a new version with a fix for this. Note that this is a pre-release. To install it, activate the acdc environment and run the command pip install "cellacdc==1.4.0rc1". If you are still having issues, try recreating the environment from scratch. To do so, deactivate the environment with conda deactivate, then remove the environment with conda env remove -n acdc and start from scratch.

Here are some more details of why you got those errors.

Unfortunately, the normal installation of v1.3.0 of Cell-ACDC onto Mac M1 or M2 does not work. You can see another discussion here.

The reason is that the installation of the GUI library PyQt5 from pip on Apple Silicon Macs does not work and I don't think the developer wants to fix that. There is a workaround by installing Cell-ACDC without dependencies and installing PyQt5 from conda with conda install pyqt, but I implemented a much better solution.

Basically, since v1.4.0, Cell-ACDC uses PyQt6 by default on Windows and PyQt5 from conda on Apple Silicon Macs. I have a Mac M1 myself and I'm testing PyQt6. Once I'm happy with that we will switch to PyQt6 on Mac too.

Note that while Cell-ACDC is installed from pip, I still recommend using conda to create the environment.

Long story short, I just released v1.4.0rc1 which implements the fix I mentioned. Note that I would have liked to test this version a bit longer before releasing it but I don't think Apple Silicon users can wait any longer. This is also the reason why it's called rc1 which means release-candidate.

Whenever you have time, please, report any issue you find so that we get closer to a stable 1.4.0 release.

Let me know how it goes and thank you very much for your patience!

Best, Francesco

makotojohira commented 1 year ago

Thank you! Will do!

Makoto Ohira Rhind Lab https://www.umassmed.edu/rhindlab/ Department of Biochemistry and Molecular Biotechnology University of Massachusetts Chan Medical School LRB 940D 364 Plantation Street Worcester, MA 01655

From: Francesco Padovani @.> Sent: Wednesday, August 2, 2023 3:39 AM To: SchmollerLab/Cell_ACDC @.> Cc: Ohira, Makoto @.>; Mention @.> Subject: Re: [SchmollerLab/Cell_ACDC] Installing javabridge - did not complete (Issue #382)

Hi Makoto,

I just released a new version with a fix for this. Note that this is a pre-release. To install it, activate the acdc environment and run the command pip install cellacdc==1.4.0rc1. If you are still having issues, try recreating the environment from scratch. To do so, deactivate the environment with conda deactivate, then remove the environment with conda env remove -n acdc and start from scratch.

Here are some more details of why you got those errors.

Unfortunately, the normal installation of v1.3.0 of Cell-ACDC onto Mac M1 or M2 does not work. You can see another discussion herehttps://github.com/SchmollerLab/Cell_ACDC/discussions/320.

The reason is that the installation of the GUI library PyQt5 from pip on Apple Silicon Macs does not work and I don't think the developer wants to fix that. There is a workaround by installing Cell-ACDC without dependencies and installing PyQt5 from conda with conda install pyqt, but I implemented a much better solution.

Basically, since v1.4.0, Cell-ACDC uses PyQt6 by default, while it will still support PyQt5. I have a Mac M1 myself and PyQt6 installation from pip seems to work without issues.

Note that while Cell-ACDC is installed from pip, I still recommend using conda to create the environment.

Long story short, I just released v1.4.0rc1 which implements the fix I mentioned. Note that I would have liked to test this version a bit longer before releasing it but I don't think Apple Silicon users can wait any longer. This is also the reason why it's called rc1 which means release-candidate.

Whenever you have time, please, report any issue you find so that we get closer to a stable 1.4.0 release.

Let me know how it goes and thank you very much for your patience!

Best, Francesco

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github-actions[bot] commented 9 months ago

Hi there, I'm the Cell-ACDC bot :wave:. This issue had no activity for more than 180 days. For now, we have marked it as "inactive" until there is some new activity. If this issue was not solved yet, unfortunately we haven't had the time to implement it or it requires more discussion. Note that it doesn't mean it has been ignored, but a little reminder from your side would help :D. Feel free to reach out to us here or on our forum. If you think that this issue is no longer relevant, you may close it by yourself. In any case, we apologise for the inconvenience and we thank you for your patience and contributions so far!

ElpadoCan commented 9 months ago

Hi Makoto, I will close this issue but feel free to reopen it should you have more comments. Thanks!