Update Dockerfile and its README

[Bevacizumab]

The original Dockerfile has issues and is not working. Ubuntu and Python versions are not specified, and the link to Psi4 is expired. This pull request fixes the Dockerfile and updates its README.md to match.

The new configuration has been tested on an Apple Silicon Mac (M4). Customization for other platforms is straightforward and can be understood easily with the updated README.md.

Changes to Dockerfile:

1. Pin versions for Ubuntu (22.04) and Python (3.12).
2. Add WORKDIR to mount local files.
3. Set PATH with ENV.
4. Psi4 is installed with a conda command instead of wget.
5. Dependencies are installed inside of a virtual environment (fermion).
6. Reduce the number of RUN commands to reduce the number of layers.

Changes to its README.md:

1. Put some details on the Dockerfile in the first paragraph of Setting up ~.
2. Add details to customization.
3. Change docker run command and introduce a simpler way to mount local files. So some previous explanations are deleted.

[google-cla]

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[mhucka]

@Bevacizumab Thank you for this contribution! It looks like Google's bots don't have a record of an agreement to the contributor's license agreement (CLA), so please follow the instructions in the CLA bot comment earlier. (It's simple and doesn't require giving away any rights.)

[Bevacizumab]

@mhucka Thank you for checking this pull request.

I completed the CLA last week, right after I saw the bot's comment. I've just confirmed that the CLA status is green in the "Checks" tab. It seems you might have been viewing an older notification without refreshing it.

Please let me know if you have any feedback on the code changes themselves. Thank you!

[mhucka]

I completed the CLA last week, right after I saw the bot's comment. I've just confirmed that the CLA status is green in the "Checks" tab. It seems you might have been viewing an older notification without refreshing it.

Oh, great. Thanks for doing that.

Please let me know if you have any feedback on the code changes themselves. Thank you!

Yes, I will review it.

[mhucka]

@Bevacizumab Thanks again for your work. There is a problem, but it may be easy to fix.

The Anaconda terms of service requires a license for business organizations. Specifically, under section 1.b of https://www.anaconda.com/legal/terms/terms-of-service (dated 2025-07-25):

When a Business Plan is Required. You must pay for a ‘Business Plan’ Subscription from Anaconda if you are using the Platform on behalf of a for-profit organization with more than 200 total employees or contractors (including all Affiliates) and you do not qualify for free use under Section 1(a) of these Terms (When Your Use is Free).

So, OpenFermion can't use make use of conda, miniconda, or the packages from https://repo.anaconda.com/pkgs/.

However, we can use conda-forge and miniforge. Would it be possible to rewrite your Dockerfile to use the miniforge3 installer and the conda-forge channel?

[Bevacizumab]

@mhucka Thank you for detailing the issue and introducing me an alternative approach. I wasn't aware of the issue with conda for this project.

However, we can use conda-forge and miniforge. Would it be possible to rewrite your Dockerfile to use the miniforge3 installer and the conda-forge channel?

I will try to update dockerfile with conda-forge and miniforge.

Additionally, i'm planning to pin the versions of the installed five packages (openfermion, cirq, openfermioncirq, openfermionpsi4, and openfermionpyscf) to ensure the reproducibility of dockerfile. Also, I will update README for indicating one can manually change the package versions.

Due to my current schedule, I may not be able to make the changes immediately, but I expect to have it done within the next few weeks (hopefully sooner).

There is a question about the versions of ubuntu and python for this project. I have tentatively used ubuntu 22.04 and python 3.12 because FROM ubuntu and RUN apt-get install -y python3 in the original dockerfile automatically installs ubuntu 22.04 and python 3.12 in my machine. Let me know if there any preferred versions to ubuntu and python for this project. If there are no specific preferences, I will proceed with ubuntu 22.04 and python 3.12.

[Bevacizumab]

Hello @mhucka. Thank you for your patience over the last few weeks.
I'm glad to let you know that I've updated the dockerfile to use Miniforge3 and conda-forge channel.
I chose not to pin the versions of the installed packages because of the complicated dependency issues this can cause.

The latest changes have been pushed to this pull request.
Could you please take a look when you have a moment?

[Bevacizumab]

Hi @mhucka, I've just rebased my branch on top of the latest master. Sorry for the long wait.

[mhucka]

@Bevacizumab Thank you for your continued efforts on this. I've added some review comments.

I will also do a PR to update the .hadolint.yaml configuration to avoid one of the Dockerfile errors it flagged because IMHO it's more of an annoyance than a benefit.

[mhucka]

Suggested change

	It creates a Python (ver. 3.12) virtual environemnt (named `fermion`) using Miniforge and installs all dependencies within it. Psi4 is installed with a conda [command](https://psicode.org/installs/v191/).
	It creates a Python (ver. 3.12) virtual environment (named `fermion`) using Miniforge and installs all dependencies within it. Psi4 is installed with a conda [command](https://psicode.org/installs/v191/).

[mhucka]

Why does this change the default from the previous x86_64 architecture? From our experiences, x86_84-based systems are still more common than arm64 systems.

[mhucka]

This change refers to a GUI interface, correct? As far as I know, docker does not provide a GUI. There is a separate tool, Docker Desktop, that provides a GUI, but we can't assume that users will be using that. (Also, Docker Desktop has license restrictions.)

Please revert this back to CLI-based instructions.

[mhucka]

This was in the original Dockerfile, and not a new addition, but it may as well be fixed as part of this PR. The Dockerfile should not need root, so it should be possible to omit this line entirely. (I'm not sure why the original had it in the first place.) Removing the line will solve the check failure about "USER should not be root".

[mhucka]

For DL3009, I will add a configuration setting to .hadolint.yaml to disable this particular check because it's just not worth the hassle.

For DL3015, go ahead and add the recommended --no-install-recommends flag.

For DL3008, we should probably pin the versions, although there are pros and cons to doing that. One way to find out the versions that can be used is to do roughly the following:

1. switch to the x86_64 architecture as discuss in a previous comment above
2. run the docker build as-is
3. figure out what versions of the packages were installed by the build
4. edit the file to add those vesions to the apt install command.

I don't know if it's possible with apt-get install, but try to see if it will let you specify just major.minor versions, not full major.minor.patch.whatever; i.e., "12.3" instead of "12.3.0.build34" etc.