(getting-started)= Getting Started =============== These are complete instructions for students to get started working with this project for use in the course and include managing a [GitLab] repository, with automated testing etc. ## Instructions Here are the general instructions. Some steps may require additional information if you are not familiar with the associated concepts (i.e. setting up SSH keys). 1. *(Optional)* Create an account and project on [CoCalc]. If you are taking the course, then you should use the project you are invited to join as part of the course. The instructions will generally assume you are working in the [CoCalc] project, but things will probably work out-of-the-box on Linux machines or Mac OS X. (No guarantees with Windows or other platforms.) If you encounter any problems, please [file an issue]. If you plan to use [CoCalc], then either complete the remaining steps using an [Online Linux Terminal](https://cocalc.com/doc/terminal.html) in your project, or by [connecting to CoCalc with SSH](https://doc.cocalc.com/project-settings.html#ssh-keys). If you are running this on another platform, you must make sure that you have a [Conda] environment setup with `anaconda-project >= 0.8.4`. You can do this easily by installing [Miniconda], then either updating the `base` environment: ```console (base) $ conda install anaconda-project (base) $ anaconda-project ... ``` or creating a new environment with `anaconda-project`: ```console (base) $ conda create -n myenv anaconda-project (base) $ conda activate myenv (myenv) $ anaconda-project ... ```
Example session with Mac OS X ```console # Download Miniconda installer MacOSX $ curl -O https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-MacOSX-x86_64.sh % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 42.3M 100 42.3M 0 0 22.8M 0 0:00:01 0:00:01 --:--:-- 22.8M # Check that it was not corrupted with the SHA 256 value listed on the website MacOSX $ shasum -a 256 Miniconda3-py39_4.10.3-MacOSX-x86_64.sh 786de9721f43e2c7d2803144c635f5f6e4823483536dc141ccd82dbb927cd508 Miniconda3-py39_4.10.3-MacOSX-x86_64.sh # Install Miniconda in the current directory MacOSX $ bash Miniconda3-py39_4.10.3-MacOSX-x86_64.sh -b -p ./miniconda3 PREFIX=/Users/mforbes/.../miniconda3 Unpacking payload ... Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /Users/mforbes/.../miniconda3 added / updated specs: - brotlipy==0.7.0=py39h9ed2024_1003 - ca-certificates==2021.7.5=hecd8cb5_1 - certifi==2021.5.30=py39hecd8cb5_0 - cffi==1.14.6=py39h2125817_0 - chardet==4.0.0=py39hecd8cb5_1003 - conda-package-handling==1.7.3=py39h9ed2024_1 - conda==4.10.3=py39hecd8cb5_0 - cryptography==3.4.7=py39h2fd3fbb_0 - idna==2.10=pyhd3eb1b0_0 - libcxx==10.0.0=1 - libffi==3.3=hb1e8313_2 - ncurses==6.2=h0a44026_1 - openssl==1.1.1k=h9ed2024_0 - pip==21.1.3=py39hecd8cb5_0 - pycosat==0.6.3=py39h9ed2024_0 - pycparser==2.20=py_2 - pyopenssl==20.0.1=pyhd3eb1b0_1 - pysocks==1.7.1=py39hecd8cb5_0 - python.app==3=py39h9ed2024_0 - python==3.9.5=h88f2d9e_3 - readline==8.1=h9ed2024_0 - requests==2.25.1=pyhd3eb1b0_0 - ruamel_yaml==0.15.100=py39h9ed2024_0 - setuptools==52.0.0=py39hecd8cb5_0 - six==1.16.0=pyhd3eb1b0_0 - sqlite==3.36.0=hce871da_0 - tk==8.6.10=hb0a8c7a_0 - tqdm==4.61.2=pyhd3eb1b0_1 - tzdata==2021a=h52ac0ba_0 - urllib3==1.26.6=pyhd3eb1b0_1 - wheel==0.36.2=pyhd3eb1b0_0 - xz==5.2.5=h1de35cc_0 - yaml==0.2.5=haf1e3a3_0 - zlib==1.2.11=h1de35cc_3 The following NEW packages will be INSTALLED: brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003 ca-certificates pkgs/main/osx-64::ca-certificates-2021.7.5-hecd8cb5_1 certifi pkgs/main/osx-64::certifi-2021.5.30-py39hecd8cb5_0 cffi pkgs/main/osx-64::cffi-1.14.6-py39h2125817_0 chardet pkgs/main/osx-64::chardet-4.0.0-py39hecd8cb5_1003 conda pkgs/main/osx-64::conda-4.10.3-py39hecd8cb5_0 conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.7.3-py39h9ed2024_1 cryptography pkgs/main/osx-64::cryptography-3.4.7-py39h2fd3fbb_0 idna pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0 libcxx pkgs/main/osx-64::libcxx-10.0.0-1 libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2 ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1 openssl pkgs/main/osx-64::openssl-1.1.1k-h9ed2024_0 pip pkgs/main/osx-64::pip-21.1.3-py39hecd8cb5_0 pycosat pkgs/main/osx-64::pycosat-0.6.3-py39h9ed2024_0 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pyopenssl pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1 pysocks pkgs/main/osx-64::pysocks-1.7.1-py39hecd8cb5_0 python pkgs/main/osx-64::python-3.9.5-h88f2d9e_3 python.app pkgs/main/osx-64::python.app-3-py39h9ed2024_0 readline pkgs/main/osx-64::readline-8.1-h9ed2024_0 requests pkgs/main/noarch::requests-2.25.1-pyhd3eb1b0_0 ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.100-py39h9ed2024_0 setuptools pkgs/main/osx-64::setuptools-52.0.0-py39hecd8cb5_0 six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0 sqlite pkgs/main/osx-64::sqlite-3.36.0-hce871da_0 tk pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0 tqdm pkgs/main/noarch::tqdm-4.61.2-pyhd3eb1b0_1 tzdata pkgs/main/noarch::tzdata-2021a-h52ac0ba_0 urllib3 pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1 wheel pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0 xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0 yaml pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0 zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3 Preparing transaction: done Executing transaction: - done installation finished. # Check the sizes MacOSX $ du -sh * 42M Miniconda3-py39_4.10.3-MacOSX-x86_64.sh 208M miniconda3 # Activate the base environment MacOSX $ . miniconda3/bin/activate (base) MacOSX $ which conda /Users/mforbes/.../tmp/miniconda3/bin/conda # Optional: initialize your shell - modifies ~/.bash_profile (base) MacOSX $ conda init no change /Users/mforbes/.../tmp/miniconda3/condabin/conda ... modified /Users/mforbes/.bash_profile # Install anaconda-project in the base environment (base) MacOSX $ conda install -qy anaconda-project Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/mforbes/.../tmp/miniconda3 added / updated specs: - anaconda-project The following packages will be downloaded: package | build ---------------------------|----------------- anaconda-client-1.8.0 | py39hecd8cb5_0 153 KB anaconda-project-0.10.1 | pyhd3eb1b0_0 218 KB attrs-21.2.0 | pyhd3eb1b0_0 46 KB clyent-1.2.2 | py39hecd8cb5_1 21 KB conda-pack-0.6.0 | pyhd3eb1b0_0 29 KB importlib-metadata-3.10.0 | py39hecd8cb5_0 33 KB ipython_genutils-0.2.0 | pyhd3eb1b0_1 27 KB jsonschema-3.2.0 | py_2 47 KB jupyter_core-4.7.1 | py39hecd8cb5_0 68 KB markupsafe-2.0.1 | py39h9ed2024_0 20 KB nbformat-5.1.3 | pyhd3eb1b0_0 44 KB pytz-2021.1 | pyhd3eb1b0_0 181 KB pyyaml-5.4.1 | py39h9ed2024_1 170 KB tornado-6.1 | py39h9ed2024_0 587 KB traitlets-5.0.5 | pyhd3eb1b0_0 81 KB zipp-3.5.0 | pyhd3eb1b0_0 13 KB ------------------------------------------------------------ Total: 1.7 MB The following NEW packages will be INSTALLED: anaconda-client pkgs/main/osx-64::anaconda-client-1.8.0-py39hecd8cb5_0 anaconda-project pkgs/main/noarch::anaconda-project-0.10.1-pyhd3eb1b0_0 attrs pkgs/main/noarch::attrs-21.2.0-pyhd3eb1b0_0 clyent pkgs/main/osx-64::clyent-1.2.2-py39hecd8cb5_1 conda-pack pkgs/main/noarch::conda-pack-0.6.0-pyhd3eb1b0_0 importlib-metadata pkgs/main/osx-64::importlib-metadata-3.10.0-py39hecd8cb5_0 importlib_metadata pkgs/main/noarch::importlib_metadata-3.10.0-hd3eb1b0_0 ipython_genutils pkgs/main/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1 jinja2 pkgs/main/noarch::jinja2-3.0.1-pyhd3eb1b0_0 jsonschema pkgs/main/noarch::jsonschema-3.2.0-py_2 jupyter_core pkgs/main/osx-64::jupyter_core-4.7.1-py39hecd8cb5_0 markupsafe pkgs/main/osx-64::markupsafe-2.0.1-py39h9ed2024_0 nbformat pkgs/main/noarch::nbformat-5.1.3-pyhd3eb1b0_0 pyrsistent pkgs/main/osx-64::pyrsistent-0.18.0-py39h9ed2024_0 python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 pytz pkgs/main/noarch::pytz-2021.1-pyhd3eb1b0_0 pyyaml pkgs/main/osx-64::pyyaml-5.4.1-py39h9ed2024_1 tornado pkgs/main/osx-64::tornado-6.1-py39h9ed2024_0 traitlets pkgs/main/noarch::traitlets-5.0.5-pyhd3eb1b0_0 zipp pkgs/main/noarch::zipp-3.5.0-pyhd3eb1b0_0 The following packages will be UPDATED: openssl 1.1.1k-h9ed2024_0 --> 1.1.1l-h9ed2024_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done # Check disk usage (base) MacOSX $ du -sh * 42M Miniconda3-py39_4.10.3-MacOSX-x86_64.sh 247M miniconda3 # Optional: Clean up downloaded packages (base) MacOSX $ rm Miniconda3-py39_4.10.3-MacOSX-x86_64.sh (base) MacOSX $ conda clean --all -y ... (base) MacOSX $ du -sh * 191M miniconda3 # Alternatively, create a new environment (base) MacOSX $ conda create -qy -n myenv anaconda-project Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/mforbes/current/courses/581/Course/tmp/miniconda3/envs/myenv added / updated specs: - anaconda-project The following packages will be downloaded: package | build ---------------------------|----------------- anaconda-client-1.8.0 | py39hecd8cb5_0 153 KB anaconda-project-0.10.1 | pyhd3eb1b0_0 218 KB attrs-21.2.0 | pyhd3eb1b0_0 46 KB clyent-1.2.2 | py39hecd8cb5_1 21 KB conda-pack-0.6.0 | pyhd3eb1b0_0 29 KB importlib-metadata-3.10.0 | py39hecd8cb5_0 33 KB importlib_metadata-3.10.0 | hd3eb1b0_0 11 KB ipython_genutils-0.2.0 | pyhd3eb1b0_1 27 KB jsonschema-3.2.0 | py_2 47 KB jupyter_core-4.7.1 | py39hecd8cb5_0 68 KB markupsafe-2.0.1 | py39h9ed2024_0 20 KB nbformat-5.1.3 | pyhd3eb1b0_0 44 KB pytz-2021.1 | pyhd3eb1b0_0 181 KB pyyaml-5.4.1 | py39h9ed2024_1 170 KB tornado-6.1 | py39h9ed2024_0 587 KB traitlets-5.0.5 | pyhd3eb1b0_0 81 KB zipp-3.5.0 | pyhd3eb1b0_0 13 KB ------------------------------------------------------------ Total: 1.7 MB The following NEW packages will be INSTALLED: anaconda-client pkgs/main/osx-64::anaconda-client-1.8.0-py39hecd8cb5_0 anaconda-project pkgs/main/noarch::anaconda-project-0.10.1-pyhd3eb1b0_0 attrs pkgs/main/noarch::attrs-21.2.0-pyhd3eb1b0_0 brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003 ca-certificates pkgs/main/osx-64::ca-certificates-2021.7.5-hecd8cb5_1 certifi pkgs/main/osx-64::certifi-2021.5.30-py39hecd8cb5_0 cffi pkgs/main/osx-64::cffi-1.14.6-py39h2125817_0 charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0 clyent pkgs/main/osx-64::clyent-1.2.2-py39hecd8cb5_1 conda-pack pkgs/main/noarch::conda-pack-0.6.0-pyhd3eb1b0_0 cryptography pkgs/main/osx-64::cryptography-3.4.7-py39h2fd3fbb_0 idna pkgs/main/noarch::idna-3.2-pyhd3eb1b0_0 importlib-metadata pkgs/main/osx-64::importlib-metadata-3.10.0-py39hecd8cb5_0 importlib_metadata pkgs/main/noarch::importlib_metadata-3.10.0-hd3eb1b0_0 ipython_genutils pkgs/main/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1 jinja2 pkgs/main/noarch::jinja2-3.0.1-pyhd3eb1b0_0 jsonschema pkgs/main/noarch::jsonschema-3.2.0-py_2 jupyter_core pkgs/main/osx-64::jupyter_core-4.7.1-py39hecd8cb5_0 libcxx pkgs/main/osx-64::libcxx-10.0.0-1 libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2 markupsafe pkgs/main/osx-64::markupsafe-2.0.1-py39h9ed2024_0 nbformat pkgs/main/noarch::nbformat-5.1.3-pyhd3eb1b0_0 ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1 openssl pkgs/main/osx-64::openssl-1.1.1l-h9ed2024_0 pip pkgs/main/osx-64::pip-21.2.4-py37hecd8cb5_0 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pyopenssl pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1 pyrsistent pkgs/main/osx-64::pyrsistent-0.18.0-py39h9ed2024_0 pysocks pkgs/main/osx-64::pysocks-1.7.1-py39hecd8cb5_0 python pkgs/main/osx-64::python-3.9.6-h88f2d9e_1 python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 pytz pkgs/main/noarch::pytz-2021.1-pyhd3eb1b0_0 pyyaml pkgs/main/osx-64::pyyaml-5.4.1-py39h9ed2024_1 readline pkgs/main/osx-64::readline-8.1-h9ed2024_0 requests pkgs/main/noarch::requests-2.26.0-pyhd3eb1b0_0 ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.100-py39h9ed2024_0 setuptools pkgs/main/osx-64::setuptools-52.0.0-py39hecd8cb5_0 six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0 sqlite pkgs/main/osx-64::sqlite-3.36.0-hce871da_0 tk pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0 tornado pkgs/main/osx-64::tornado-6.1-py39h9ed2024_0 tqdm pkgs/main/noarch::tqdm-4.62.1-pyhd3eb1b0_1 traitlets pkgs/main/noarch::traitlets-5.0.5-pyhd3eb1b0_0 tzdata pkgs/main/noarch::tzdata-2021a-h5d7bf9c_0 urllib3 pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1 wheel pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_0 xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0 yaml pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0 zipp pkgs/main/noarch::zipp-3.5.0-pyhd3eb1b0_0 zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done (base) MacOSX $ conda activate myenv (myenv) MacOSX $ type python3 python3 is /Users/mforbes/.../tmp/miniconda3/envs/myenv/bin/python3 # Optionally clean: (myenv) MacOSX $ conda clean --all -y ... (myenv) MacOSX $ du -sh * 278M miniconda3 ```
2. Clone this repo and change directories to enter the project: ```bash git clone https://gitlab.com/wsu-courses/physics-581-physics-inspired-computation.git cd physics-581-physics-inspired-computation ``` *Note: I actually prefer to use [Mercurial] and usually use the [hg-git] plugin, but don't recommend this unless you are very familiar with [Mercurial]. See {ref}`sec:version-control` for more details:* ```bash hg clone https://gitlab.com/wsu-courses/physics-581-physics-inspired-computation.git cd physics-581-physics-inspired-computation ``` 3. Use [`anaconda-project`](https://anaconda-project.readthedocs.io/en/latest/) to provision the environment, setup the kernel, clone the resources, etc. This can all be done with: ```bash make init ``` Which will do the following: 1. Clone the [Resources project] project into `_ext/Resources`. Note: this is private and requires that your instructor grant you access. 2. Run `anaconda-project prepare` which uses `conda` or `mamba` to create an environment in `envs/phys-581` as specified in the `anaconda-project.yaml` file. *(This may take some time when you first run it, and consumes about 2GB of disk space. You can clean up some space after by running `make clean`.)* 3. Installs this environment as an [IPython kernel](https://ipython.readthedocs.io/en/stable/install/kernel_install.html) called `phys-581` for use with [Jupyter]. This is done by running `anaconda-project run init` which runs [`ipykernel install`](https://ipython.readthedocs.io/en/stable/install/kernel_install.html): see the `init` target in `anaconda-project.yml` for details. 4. If you are on [CoCalc] *(technically, if `ANACONDA2020` is defined)*, then `make init` will also install the `mmf-setup` package, update some files, create a `~/.bash_aliases` file, and insert a line to activate the environment when logging in. This also then runs `make sync` which uses [Jupytext] to populate the notebooks so you can use them with [CoCalc].
Example session on Mac OS X In the following, I have already authenticated to my SSH keys which I have registered at [GitLab], so there is no need for passwords. ```console (myenv) MacOSX $ git clone git@gitlab.com:wsu-courses/physics-581-physics-inspired-computation.git Cloning into 'physics-581-physics-inspired-computation'... remote: Enumerating objects: 269, done. remote: Counting objects: 100% (98/98), done. remote: Compressing objects: 100% (59/59), done. remote: Total 269 (delta 53), reused 76 (delta 39), pack-reused 171 Receiving objects: 100% (269/269), 201.54 KiB | 1.10 MiB/s, done. Resolving deltas: 100% (129/129), done. (myenv) MacOSX $ cd physics-581-physics-inspired-computation (myenv) MacOSX $ ls Docs Notes.md Resources anaconda-project.yaml poetry.lock tests Makefile README.md Topics phys_581 pyproject.toml (myenv) MacOSX $ make init $ make init git clone git@gitlab.com:wsu-courses/physics-581-physics-inspired-computation_resources.git _ext/Resources Cloning into '_ext/Resources'... remote: Enumerating objects: 10, done. remote: Counting objects: 100% (10/10), done. remote: Compressing objects: 100% (9/9), done. remote: Total 10 (delta 0), reused 0 (delta 0), pack-reused 0 Receiving objects: 100% (10/10), 20.22 MiB | 8.09 MiB/s, done. CONDA_EXE=/data/apps/conda/bin/conda anaconda-project prepare Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/mforbes/.../tmp/physics-581-physics-inspired-computation/envs/phys-581 added / updated specs: - anaconda-project[version='>=0.10.1'] - black - conda-forge::myst-nb - conda-forge::sphinx-autobuild - conda-forge::sphinx-book-theme - conda-forge::sphinx-panels - conda-forge::uncertainties - jupytext - matplotlib - pandas - pip - pytest-cov - pytest-flake8 - pytest-xdist - python=3.9 - scipy - sphinx The following packages will be downloaded: package | build ---------------------------|----------------- blas-1.0 | mkl 6 KB importlib_metadata-3.10.0 | hd3eb1b0_0 11 KB matplotlib-3.4.2 | py39hecd8cb5_0 26 KB numpy-1.20.3 | py39h4b4dc7a_0 23 KB python_abi-3.9 | 2_cp39 4 KB conda-forge typing-extensions-3.10.0.0 | hd3eb1b0_0 8 KB ------------------------------------------------------------ Total: 78 KB The following NEW packages will be INSTALLED: alabaster pkgs/main/noarch::alabaster-0.7.12-pyhd3eb1b0_0 anaconda-client pkgs/main/osx-64::anaconda-client-1.8.0-py39hecd8cb5_0 anaconda-project pkgs/main/noarch::anaconda-project-0.10.1-pyhd3eb1b0_0 anyio pkgs/main/osx-64::anyio-2.2.0-py39hecd8cb5_1 appdirs pkgs/main/noarch::appdirs-1.4.4-py_0 appnope pkgs/main/osx-64::appnope-0.1.2-py39hecd8cb5_1001 argon2-cffi pkgs/main/osx-64::argon2-cffi-20.1.0-py39h9ed2024_1 async_generator pkgs/main/noarch::async_generator-1.10-pyhd3eb1b0_0 attrs pkgs/main/noarch::attrs-20.3.0-pyhd3eb1b0_0 babel pkgs/main/noarch::babel-2.9.1-pyhd3eb1b0_0 backcall pkgs/main/noarch::backcall-0.2.0-pyhd3eb1b0_0 beautifulsoup4 pkgs/main/noarch::beautifulsoup4-4.9.3-pyha847dfd_0 black pkgs/main/noarch::black-19.10b0-py_0 blas pkgs/main/osx-64::blas-1.0-mkl bleach pkgs/main/noarch::bleach-4.0.0-pyhd3eb1b0_0 bottleneck pkgs/main/osx-64::bottleneck-1.3.2-py39he3068b8_1 brotli pkgs/main/osx-64::brotli-1.0.9-hb1e8313_2 brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003 ca-certificates pkgs/main/osx-64::ca-certificates-2021.7.5-hecd8cb5_1 certifi pkgs/main/osx-64::certifi-2021.5.30-py39hecd8cb5_0 cffi pkgs/main/osx-64::cffi-1.14.6-py39h2125817_0 charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0 click pkgs/main/noarch::click-8.0.1-pyhd3eb1b0_0 click-completion conda-forge/osx-64::click-completion-0.5.2-py39h6e9494a_2 click-log conda-forge/noarch::click-log-0.3.2-pyh9f0ad1d_0 clyent pkgs/main/osx-64::clyent-1.2.2-py39hecd8cb5_1 colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0 conda-pack pkgs/main/noarch::conda-pack-0.6.0-pyhd3eb1b0_0 coverage pkgs/main/osx-64::coverage-5.5-py39h9ed2024_2 cryptography pkgs/main/osx-64::cryptography-3.4.7-py39h2fd3fbb_0 cycler pkgs/main/osx-64::cycler-0.10.0-py39hecd8cb5_0 debugpy pkgs/main/osx-64::debugpy-1.4.1-py39h23ab428_0 decorator pkgs/main/noarch::decorator-5.0.9-pyhd3eb1b0_0 defusedxml pkgs/main/noarch::defusedxml-0.7.1-pyhd3eb1b0_0 docutils pkgs/main/osx-64::docutils-0.16-py39hecd8cb5_1 entrypoints pkgs/main/osx-64::entrypoints-0.3-py39hecd8cb5_0 execnet pkgs/main/noarch::execnet-1.9.0-pyhd3eb1b0_0 flake8 pkgs/main/noarch::flake8-3.9.2-pyhd3eb1b0_0 fonttools pkgs/main/noarch::fonttools-4.25.0-pyhd3eb1b0_0 freetype pkgs/main/osx-64::freetype-2.10.4-ha233b18_0 future pkgs/main/osx-64::future-0.18.2-py39hecd8cb5_1 gitdb pkgs/main/noarch::gitdb-4.0.7-pyhd3eb1b0_0 gitpython pkgs/main/noarch::gitpython-3.1.18-pyhd3eb1b0_1 greenlet pkgs/main/osx-64::greenlet-1.1.1-py39h23ab428_0 idna pkgs/main/noarch::idna-3.2-pyhd3eb1b0_0 imagesize pkgs/main/noarch::imagesize-1.2.0-pyhd3eb1b0_0 importlib-metadata pkgs/main/osx-64::importlib-metadata-3.10.0-py39hecd8cb5_0 importlib_metadata pkgs/main/noarch::importlib_metadata-3.10.0-hd3eb1b0_0 importlib_resourc~ pkgs/main/osx-64::importlib_resources-3.3.1-py39hecd8cb5_0 iniconfig pkgs/main/noarch::iniconfig-1.1.1-pyhd3eb1b0_0 intel-openmp pkgs/main/osx-64::intel-openmp-2021.3.0-hecd8cb5_3375 ipykernel pkgs/main/osx-64::ipykernel-6.2.0-py39hecd8cb5_1 ipython pkgs/main/osx-64::ipython-7.26.0-py39h01d92e1_0 ipython_genutils pkgs/main/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1 ipywidgets pkgs/main/noarch::ipywidgets-7.6.3-pyhd3eb1b0_1 jedi pkgs/main/osx-64::jedi-0.18.0-py39hecd8cb5_1 jinja2 pkgs/main/noarch::jinja2-3.0.1-pyhd3eb1b0_0 jpeg pkgs/main/osx-64::jpeg-9b-he5867d9_2 jsonschema pkgs/main/noarch::jsonschema-3.2.0-py_2 jupyter-cache conda-forge/noarch::jupyter-cache-0.4.3-pyhd8ed1ab_0 jupyter-server-ma~ conda-forge/noarch::jupyter-server-mathjax-0.2.3-pyhd8ed1ab_0 jupyter-sphinx conda-forge/noarch::jupyter-sphinx-0.3.2-py_0 jupyter_client pkgs/main/noarch::jupyter_client-6.1.12-pyhd3eb1b0_0 jupyter_core pkgs/main/osx-64::jupyter_core-4.7.1-py39hecd8cb5_0 jupyter_server pkgs/main/osx-64::jupyter_server-1.4.1-py39hecd8cb5_0 jupyterlab_widgets pkgs/main/noarch::jupyterlab_widgets-1.0.0-pyhd3eb1b0_1 jupytext conda-forge/noarch::jupytext-1.11.1-pyh44b312d_0 kiwisolver pkgs/main/osx-64::kiwisolver-1.3.1-py39h23ab428_0 lcms2 pkgs/main/osx-64::lcms2-2.12-hf1fd2bf_0 libcxx pkgs/main/osx-64::libcxx-10.0.0-1 libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2 libgfortran pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2 libpng pkgs/main/osx-64::libpng-1.6.37-ha441bb4_0 libsodium pkgs/main/osx-64::libsodium-1.0.18-h1de35cc_0 libtiff pkgs/main/osx-64::libtiff-4.2.0-h87d7836_0 libwebp-base pkgs/main/osx-64::libwebp-base-1.2.0-h9ed2024_0 livereload conda-forge/noarch::livereload-2.6.3-pyh9f0ad1d_0 lz4-c pkgs/main/osx-64::lz4-c-1.9.3-h23ab428_1 markdown-it-py conda-forge/noarch::markdown-it-py-0.6.2-pyhd8ed1ab_0 markupsafe pkgs/main/osx-64::markupsafe-2.0.1-py39h9ed2024_0 matplotlib pkgs/main/osx-64::matplotlib-3.4.2-py39hecd8cb5_0 matplotlib-base pkgs/main/osx-64::matplotlib-base-3.4.2-py39h8b3ea08_0 matplotlib-inline pkgs/main/noarch::matplotlib-inline-0.1.2-pyhd3eb1b0_2 mccabe 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pkgs/main/noarch::nest-asyncio-1.5.1-pyhd3eb1b0_0 notebook pkgs/main/osx-64::notebook-6.4.3-py39hecd8cb5_0 numexpr pkgs/main/osx-64::numexpr-2.7.3-py39h5873af2_1 numpy pkgs/main/osx-64::numpy-1.20.3-py39h4b4dc7a_0 numpy-base pkgs/main/osx-64::numpy-base-1.20.3-py39he0bd621_0 olefile pkgs/main/noarch::olefile-0.46-py_0 openjpeg pkgs/main/osx-64::openjpeg-2.4.0-h66ea3da_0 openssl pkgs/main/osx-64::openssl-1.1.1l-h9ed2024_0 packaging pkgs/main/noarch::packaging-21.0-pyhd3eb1b0_0 pandas pkgs/main/osx-64::pandas-1.3.2-py39h5008ddb_0 pandoc pkgs/main/osx-64::pandoc-2.12-hecd8cb5_0 pandocfilters pkgs/main/osx-64::pandocfilters-1.4.3-py39hecd8cb5_1 parso pkgs/main/noarch::parso-0.8.2-pyhd3eb1b0_0 pathspec pkgs/main/noarch::pathspec-0.7.0-py_0 pexpect pkgs/main/noarch::pexpect-4.8.0-pyhd3eb1b0_3 pickleshare pkgs/main/noarch::pickleshare-0.7.5-pyhd3eb1b0_1003 pillow pkgs/main/osx-64::pillow-8.3.1-py39ha4cf6ea_0 pip pkgs/main/osx-64::pip-21.2.4-py37hecd8cb5_0 pluggy pkgs/main/osx-64::pluggy-0.13.1-py39hecd8cb5_0 prometheus_client pkgs/main/noarch::prometheus_client-0.11.0-pyhd3eb1b0_0 prompt-toolkit pkgs/main/noarch::prompt-toolkit-3.0.17-pyh06a4308_0 ptyprocess pkgs/main/noarch::ptyprocess-0.7.0-pyhd3eb1b0_2 py pkgs/main/noarch::py-1.10.0-pyhd3eb1b0_0 pycodestyle pkgs/main/noarch::pycodestyle-2.7.0-pyhd3eb1b0_0 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pydata-sphinx-the~ conda-forge/noarch::pydata-sphinx-theme-0.6.3-pyhd8ed1ab_0 pyflakes pkgs/main/noarch::pyflakes-2.3.1-pyhd3eb1b0_0 pygments pkgs/main/noarch::pygments-2.10.0-pyhd3eb1b0_0 pyopenssl pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1 pyparsing pkgs/main/noarch::pyparsing-2.4.7-pyhd3eb1b0_0 pyrsistent pkgs/main/osx-64::pyrsistent-0.18.0-py39h9ed2024_0 pysocks pkgs/main/osx-64::pysocks-1.7.1-py39hecd8cb5_0 pytest pkgs/main/osx-64::pytest-6.2.4-py39hecd8cb5_2 pytest-cov pkgs/main/noarch::pytest-cov-2.12.1-pyhd3eb1b0_0 pytest-flake8 pkgs/main/noarch::pytest-flake8-1.0.7-pyhd3eb1b0_0 pytest-forked pkgs/main/noarch::pytest-forked-1.3.0-pyhd3eb1b0_0 pytest-xdist pkgs/main/noarch::pytest-xdist-2.3.0-pyhd3eb1b0_0 python pkgs/main/osx-64::python-3.9.6-h88f2d9e_1 python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 python_abi conda-forge/osx-64::python_abi-3.9-2_cp39 pytz pkgs/main/noarch::pytz-2021.1-pyhd3eb1b0_0 pyyaml pkgs/main/osx-64::pyyaml-5.4.1-py39h9ed2024_1 pyzmq pkgs/main/osx-64::pyzmq-22.2.1-py39h23ab428_1 readline pkgs/main/osx-64::readline-8.1-h9ed2024_0 regex pkgs/main/osx-64::regex-2021.8.3-py39h9ed2024_0 requests pkgs/main/noarch::requests-2.26.0-pyhd3eb1b0_0 ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.100-py39h9ed2024_0 scipy pkgs/main/osx-64::scipy-1.6.2-py39hd5f7400_1 send2trash pkgs/main/noarch::send2trash-1.5.0-pyhd3eb1b0_1 setuptools pkgs/main/osx-64::setuptools-52.0.0-py39hecd8cb5_0 shellingham pkgs/main/noarch::shellingham-1.3.1-py_0 six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0 smmap pkgs/main/noarch::smmap-4.0.0-pyhd3eb1b0_0 sniffio pkgs/main/osx-64::sniffio-1.2.0-py39hecd8cb5_1 snowballstemmer pkgs/main/noarch::snowballstemmer-2.1.0-pyhd3eb1b0_0 soupsieve pkgs/main/noarch::soupsieve-2.2.1-pyhd3eb1b0_0 sphinx pkgs/main/noarch::sphinx-3.5.4-pyhd3eb1b0_0 sphinx-autobuild conda-forge/noarch::sphinx-autobuild-2021.3.14-pyhd8ed1ab_0 sphinx-book-theme conda-forge/noarch::sphinx-book-theme-0.1.3-pyhd8ed1ab_0 sphinx-panels conda-forge/noarch::sphinx-panels-0.6.0-pyhd8ed1ab_0 sphinx-togglebutt~ conda-forge/noarch::sphinx-togglebutton-0.2.3-pyhd3deb0d_0 sphinxcontrib-app~ pkgs/main/noarch::sphinxcontrib-applehelp-1.0.2-pyhd3eb1b0_0 sphinxcontrib-dev~ pkgs/main/noarch::sphinxcontrib-devhelp-1.0.2-pyhd3eb1b0_0 sphinxcontrib-htm~ pkgs/main/noarch::sphinxcontrib-htmlhelp-2.0.0-pyhd3eb1b0_0 sphinxcontrib-jsm~ pkgs/main/noarch::sphinxcontrib-jsmath-1.0.1-pyhd3eb1b0_0 sphinxcontrib-qth~ pkgs/main/noarch::sphinxcontrib-qthelp-1.0.3-pyhd3eb1b0_0 sphinxcontrib-ser~ pkgs/main/noarch::sphinxcontrib-serializinghtml-1.1.5-pyhd3eb1b0_0 sqlalchemy pkgs/main/osx-64::sqlalchemy-1.4.22-py39h9ed2024_0 sqlite pkgs/main/osx-64::sqlite-3.36.0-hce871da_0 terminado pkgs/main/osx-64::terminado-0.9.4-py39hecd8cb5_0 testpath pkgs/main/noarch::testpath-0.5.0-pyhd3eb1b0_0 tk pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0 toml pkgs/main/noarch::toml-0.10.2-pyhd3eb1b0_0 tornado pkgs/main/osx-64::tornado-6.1-py39h9ed2024_0 tqdm pkgs/main/noarch::tqdm-4.62.1-pyhd3eb1b0_1 traitlets pkgs/main/noarch::traitlets-5.0.5-pyhd3eb1b0_0 typed-ast pkgs/main/osx-64::typed-ast-1.4.3-py39h9ed2024_1 typing-extensions pkgs/main/noarch::typing-extensions-3.10.0.0-hd3eb1b0_0 typing_extensions pkgs/main/noarch::typing_extensions-3.10.0.0-pyh06a4308_0 tzdata pkgs/main/noarch::tzdata-2021a-h5d7bf9c_0 uncertainties conda-forge/noarch::uncertainties-3.1.6-pyhd8ed1ab_0 urllib3 pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1 wcwidth pkgs/main/noarch::wcwidth-0.2.5-py_0 webencodings pkgs/main/osx-64::webencodings-0.5.1-py39hecd8cb5_1 wheel pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_0 widgetsnbextension pkgs/main/osx-64::widgetsnbextension-3.5.1-py39hecd8cb5_0 xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0 yaml pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0 zeromq pkgs/main/osx-64::zeromq-4.3.4-h23ab428_0 zipp pkgs/main/noarch::zipp-3.5.0-pyhd3eb1b0_0 zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3 zstd pkgs/main/osx-64::zstd-1.4.9-h322a384_0 Downloading and Extracting Packages typing-extensions-3. | 8 KB | ########## | 100% importlib_metadata-3 | 11 KB | ########## | 100% matplotlib-3.4.2 | 26 KB | ########## | 100% blas-1.0 | 6 KB | ########## | 100% python_abi-3.9 | 4 KB | ########## | 100% numpy-1.20.3 | 23 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done # # To activate this environment, use # # $ conda activate /Users/mforbes/.../physics-581-physics-inspired-computation/envs/phys-581 # # To deactivate an active environment, use # # $ conda deactivate Collecting sphinxcontrib-bibtex Using cached sphinxcontrib_bibtex-2.3.0-py3-none-any.whl (35 kB) Collecting mmf-setup Using cached mmf_setup-0.4.3-py3-none-any.whl (73 kB) Collecting sphinxcontrib-zopeext Using cached sphinxcontrib_zopeext-0.2.4-py3-none-any.whl Collecting pybtex>=0.20 Using cached pybtex-0.24.0-py2.py3-none-any.whl (561 kB) Collecting pybtex-docutils>=1.0.0 Using cached pybtex_docutils-1.0.1-py3-none-any.whl (4.8 kB) Requirement already satisfied: Sphinx>=2.1 in ./envs/phys-581/lib/python3.9/site-packages (from sphinxcontrib-bibtex) (3.5.4) Requirement already satisfied: docutils>=0.8 in ./envs/phys-581/lib/python3.9/site-packages (from sphinxcontrib-bibtex) (0.16) Collecting tomlkit Using cached tomlkit-0.7.2-py2.py3-none-any.whl (32 kB) Requirement already satisfied: importlib-metadata in ./envs/phys-581/lib/python3.9/site-packages (from mmf-setup) (3.10.0) Collecting zope.interface Using cached zope.interface-5.4.0-cp39-cp39-macosx_10_14_x86_64.whl (208 kB) Collecting latexcodec>=1.0.4 Using cached latexcodec-2.0.1-py2.py3-none-any.whl (18 kB) Requirement already satisfied: PyYAML>=3.01 in ./envs/phys-581/lib/python3.9/site-packages (from pybtex>=0.20->sphinxcontrib-bibtex) (5.4.1) Requirement already satisfied: six in ./envs/phys-581/lib/python3.9/site-packages (from pybtex>=0.20->sphinxcontrib-bibtex) (1.16.0) Requirement already satisfied: babel>=1.3 in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (2.9.1) Requirement already satisfied: sphinxcontrib-htmlhelp in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (2.0.0) Requirement already satisfied: requests>=2.5.0 in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (2.26.0) Requirement already satisfied: Pygments>=2.0 in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (2.10.0) Requirement already satisfied: sphinxcontrib-devhelp in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (1.0.2) Requirement already satisfied: imagesize in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (1.2.0) Requirement already satisfied: alabaster<0.8,>=0.7 in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (0.7.12) Requirement already satisfied: sphinxcontrib-serializinghtml in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (1.1.5) Requirement already satisfied: Jinja2>=2.3 in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (3.0.1) Requirement already satisfied: sphinxcontrib-jsmath in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (1.0.1) Requirement already satisfied: sphinxcontrib-applehelp in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (1.0.2) Requirement already satisfied: snowballstemmer>=1.1 in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (2.1.0) Requirement already satisfied: setuptools in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (52.0.0.post20210125) Requirement already satisfied: packaging in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (21.0) Requirement already satisfied: sphinxcontrib-qthelp in ./envs/phys-581/lib/python3.9/site-packages (from Sphinx>=2.1->sphinxcontrib-bibtex) (1.0.3) Requirement already satisfied: pytz>=2015.7 in ./envs/phys-581/lib/python3.9/site-packages (from babel>=1.3->Sphinx>=2.1->sphinxcontrib-bibtex) (2021.1) Requirement already satisfied: MarkupSafe>=2.0 in ./envs/phys-581/lib/python3.9/site-packages (from Jinja2>=2.3->Sphinx>=2.1->sphinxcontrib-bibtex) (2.0.1) Requirement already satisfied: idna<4,>=2.5 in ./envs/phys-581/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx>=2.1->sphinxcontrib-bibtex) (3.2) Requirement already satisfied: certifi>=2017.4.17 in ./envs/phys-581/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx>=2.1->sphinxcontrib-bibtex) (2021.5.30) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./envs/phys-581/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx>=2.1->sphinxcontrib-bibtex) (1.26.6) Requirement already satisfied: charset-normalizer~=2.0.0 in ./envs/phys-581/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx>=2.1->sphinxcontrib-bibtex) (2.0.4) Requirement already satisfied: zipp>=0.5 in ./envs/phys-581/lib/python3.9/site-packages (from importlib-metadata->mmf-setup) (3.5.0) Requirement already satisfied: pyparsing>=2.0.2 in ./envs/phys-581/lib/python3.9/site-packages (from packaging->Sphinx>=2.1->sphinxcontrib-bibtex) (2.4.7) Installing collected packages: latexcodec, pybtex, zope.interface, tomlkit, pybtex-docutils, sphinxcontrib-zopeext, sphinxcontrib-bibtex, mmf-setup Successfully installed latexcodec-2.0.1 mmf-setup-0.4.3 pybtex-0.24.0 pybtex-docutils-1.0.1 sphinxcontrib-bibtex-2.3.0 sphinxcontrib-zopeext-0.2.4 tomlkit-0.7.2 zope.interface-5.4.0 The project is ready to run commands. Use `anaconda-project list-commands` to see what's available. CONDA_EXE=/data/apps/conda/bin/conda anaconda-project run init # Custom command: see anaconda-project.yaml Installed kernelspec phys-581 in /Users/mforbes/Library/Jupyter/kernels/phys-581 # Optional: run a shell with the installed environment (myenv) MacOSX $ anaconda-project run bash bash-3.2$ type python3 python3 is /Users/mforbes/.../tmp/physics-581-physics-inspired-computation/envs/phys-581/bin/python3 # You could also do this manually by activating the environment with conda (myenv) MacOSX $ conda activate envs/phys-581/ (phys-581) MacOSX $ type python3 python3 is /Users/mforbes/.../tmp/physics-581-physics-inspired-computation/envs/phys-581/bin/python3 ```
Example session on CoCalc Before doing this, I first bought a license for my private "student" CoCalc project. I also added the User key to my `~/.ssh/config` file with the alias `smc581private`: ``` # ~/.ssh/config file ... Host smc581private User f6432a... Host smc* HostName ssh.cocalc.com ForwardAgent yes SendEnv LC_HG_USERNAME SendEnv LC_GIT_USERNAME SendEnv LC_GIT_USEREMAIL SetEnv LC_EDITOR=vi ``` Before continuing, make sure you connect to the project via the web and start it, otherwise you will get the following response: ```console MacOSX $ ssh smc581private f6432a...@ssh.cocalc.com: Permission denied (publickey). ``` After starting the project, this works (takes about 5 minutes): ```console MacOSX $ ssh smc581private ~$ git clone https://gitlab.com/wsu-courses/physics-581-physics-inspired-computation.git Cloning into 'physics-581-physics-inspired-computation'... remote: Enumerating objects: 269, done. remote: Counting objects: 100% (98/98), done. remote: Compressing objects: 100% (59/59), done. remote: Total 269 (delta 53), reused 76 (delta 39), pack-reused 171 Receiving objects: 100% (269/269), 201.54 KiB | 4.58 MiB/s, done. Resolving deltas: 100% (129/129), done. ~$ cd physics-581-physics-inspired-computation ~/physics-581-physics-inspired-computation$ time make init python3 -m pip install --user --upgrade mmf-setup Collecting mmf-setup Downloading mmf_setup-0.4.3-py3-none-any.whl (73 kB) |████████████████████████████████| 73 kB 4.7 MB/s Collecting tomlkit Downloading tomlkit-0.7.2-py2.py3-none-any.whl (32 kB) Requirement already satisfied: importlib-metadata in /usr/lib/python3/dist-packages (from mmf-setup) (1.5.0) Installing collected packages: tomlkit, mmf-setup Successfully installed mmf-setup-0.4.3 tomlkit-0.7.2 mmf_setup cocalc # Installing mercurial, hg-evolve, hg-git, jupytext for python3... python3 -m pip install --upgrade --user pip mercurial hg-evolve hg-git jupytext Requirement already satisfied: pip in /usr/local/lib/python3.8/dist-packages (21.2.4) Collecting mercurial Downloading mercurial-5.9.1.tar.gz (8.1 MB) |████████████████████████████████| 8.1 MB 2.6 MB/s Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Collecting hg-evolve Downloading hg-evolve-10.3.3.tar.gz (850 kB) |████████████████████████████████| 850 kB 66.3 MB/s Collecting hg-git Downloading hg_git-0.10.2-py3-none-any.whl (65 kB) |████████████████████████████████| 65 kB 48.8 MB/s Requirement already satisfied: jupytext in /usr/local/lib/python3.8/dist-packages (1.11.5) Requirement already satisfied: dulwich>=0.19.0 in /usr/lib/python3/dist-packages (from hg-git) (0.19.15) Requirement already satisfied: nbformat in /usr/local/lib/python3.8/dist-packages (from jupytext) (5.1.3) Requirement already satisfied: markdown-it-py~=1.0 in /usr/local/lib/python3.8/dist-packages (from jupytext) (1.0.0) Requirement already satisfied: pyyaml in /usr/lib/python3/dist-packages (from jupytext) (5.3.1) Requirement already satisfied: mdit-py-plugins in /usr/local/lib/python3.8/dist-packages (from jupytext) (0.2.4) Requirement already satisfied: toml in /usr/lib/python3/dist-packages (from jupytext) (0.10.0) Requirement already satisfied: attrs<21,>=19 in /usr/local/lib/python3.8/dist-packages (from markdown-it-py~=1.0->jupytext) (19.3.0) Requirement already satisfied: traitlets>=4.1 in /usr/local/lib/python3.8/dist-packages (from nbformat->jupytext) (5.0.5) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /usr/local/lib/python3.8/dist-packages (from nbformat->jupytext) (3.2.0) Requirement already satisfied: ipython-genutils in /usr/local/lib/python3.8/dist-packages (from nbformat->jupytext) (0.2.0) Requirement already satisfied: jupyter-core in /usr/local/lib/python3.8/dist-packages (from nbformat->jupytext) (4.6.3) Requirement already satisfied: pyrsistent>=0.14.0 in /usr/local/lib/python3.8/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat->jupytext) (0.16.0) Requirement already satisfied: setuptools in /usr/local/lib/python3.8/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat->jupytext) (57.4.0) Requirement already satisfied: six>=1.11.0 in /usr/local/lib/python3.8/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat->jupytext) (1.15.0) Building wheels for collected packages: mercurial, hg-evolve Building wheel for mercurial (PEP 517) ... done Created wheel for mercurial: filename=mercurial-5.9.1-cp38-cp38-linux_x86_64.whl size=6648296 sha256=9e819907db0cac0861851fc83d215ed29e8aa06756ffaa73fb3fcbfa5629c3bb Stored in directory: /tmp/pip-ephem-wheel-cache-9bf8f4mm/wheels/2f/b2/78/7e602145b2ba0555351230b0376f139080ae51126e77d18ace Building wheel for hg-evolve (setup.py) ... done Created wheel for hg-evolve: filename=hg_evolve-10.3.3-py3-none-any.whl size=214847 sha256=791480885a6532a7d4a211a40f8ac375d4d8a352a1605c29fc64ec7b7b73f88f Stored in directory: /tmp/pip-ephem-wheel-cache-9bf8f4mm/wheels/d4/a6/97/55c036c6a151d1735117ec1ed4ff7c3dd5d1628041a4016325 Successfully built mercurial hg-evolve Installing collected packages: mercurial, hg-git, hg-evolve Successfully installed hg-evolve-10.3.3 hg-git-0.10.2 mercurial-5.9.1 # Setting up config files for CoCalc... mv ~/.bashrc ~/.bashrc_cocalc /home/user/.local/bin/mmf_initial_setup -v /home/user/.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc Using = /home/user Using dir = /home/user/.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc Warning: No dest = 2nd line in file '/home/user/.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/README.md'... ignoring os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/bash_aliases', '/home/user/.bash_aliases') os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/bashrc', '/home/user/.bashrc') Warning: No dest = 2nd line in file '/home/user/.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/gitconfig'... ignoring os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/gitignore', '/home/user/.gitignore') os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/hgignore', '/home/user/.hgignore') os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/hgrc', '/home/user/.hgrc') os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/inputrc', '/home/user/.inputrc') Warning: No dest = 2nd line in file '/home/user/.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/message.txt'... ignoring os.symlink('../lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/mr', '/home/user/.local/bin/mr') os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/mrconfig', '/home/user/.mrconfig') os.symlink('.local/lib/python3.8/site-packages/mmf_setup/_data/config_files/cocalc/pdbrc', '/home/user/.pdbrc') Configurations for your CoCalc project have been symlinked as described above. If you use version control, then to get the most of the configuration, please make sure that you set the following variables on your personal computer, and forward them when you ssh to the project: # ~/.bashrc or similar LC_HG_USERNAME=Your Full Name LC_GIT_USEREMAIL=your.email.address+git@gmail.com LC_GIT_USERNAME=Your Full Name To forward these, your SSH config file (~/.ssh/config) might look like: # ~/.ssh/config Host cc-project1 User ff1cb986f... Host cc* HostName ssh.cocalc.com ForwardAgent yes SendEnv LC_HG_USERNAME SendEnv LC_GIT_USERNAME SendEnv LC_GIT_USEREMAIL SetEnv LC_EDITOR=vi source $ANACONDA2020/bin/activate root && CONDA_EXE=mamba anaconda-project prepare pkgs/main/noarch pkgs/r/linux-64 cvxgrp/linux-64 plotly/linux-64 pytorch/noarch pkgs/r/noarch vpython/noarch bioconda/linux-64 plotly/noarch gimli/noarch pkgs/main/linux-64 vpython/linux-64 bokeh/noarch gimli/linux-64 cvxgrp/noarch bioconda/noarch scitools/noarch astropy/noarch pytorch/linux-64 bokeh/linux-64 astropy/linux-64 scitools/linux-64 conda-forge/noarch conda-forge/linux-64 ERROR Caught a filesystem error: Read-only file system: '/ext/anaconda2020.02/pkgs/sphinxcontrib-jsmath-1.0.1-py_0' ERROR Caught a filesystem error: Read-only file system: '/ext/anaconda2020.02/pkgs/imagesize-1.2.0-py_0' Transaction Prefix: /home/user/physics-581-physics-inspired-computation/envs/phys-581 Updating specs: - scipy - conda-forge::sphinx-panels - conda-forge::sphinx-autobuild - pandas - conda-forge::sphinx-book-theme - python==3.9 - conda-forge::myst-nb - pip - anaconda-project[version='>=0.10.1'] - conda-forge::uncertainties - pytest-flake8 - matplotlib - pytest-cov - jupytext - black - pytest-xdist - sphinx Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────────────────────── _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 3 KB _openmp_mutex 4.5 1_gnu conda-forge/linux-64 22 KB alabaster 0.7.12 py_0 conda-forge/noarch 15 KB alsa-lib 1.2.3 h516909a_0 conda-forge/linux-64 560 KB anaconda-client 1.8.0 py39h06a4308_0 pkgs/main/linux-64 153 KB anaconda-project 0.10.1 pyhd8ed1ab_0 conda-forge/noarch Cached anyio 3.3.0 py39hf3d152e_0 conda-forge/linux-64 148 KB argon2-cffi 20.1.0 py39hbd71b63_2 conda-forge/linux-64 47 KB async_generator 1.10 py_0 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h9c3ff4c_0 conda-forge/linux-64 213 KB libblas 3.9.0 11_linux64_openblas conda-forge/linux-64 12 KB libcblas 3.9.0 11_linux64_openblas conda-forge/linux-64 11 KB libclang 11.1.0 default_ha53f305_1 conda-forge/linux-64 19 MB libdeflate 1.7 h7f98852_5 conda-forge/linux-64 67 KB libedit 3.1.20210714 h7f8727e_0 pkgs/main/linux-64 165 KB libevent 2.1.10 hcdb4288_3 conda-forge/linux-64 1 MB libffi 3.3 h58526e2_2 conda-forge/linux-64 51 KB libgcc-ng 11.1.0 hc902ee8_8 conda-forge/linux-64 Cached libgfortran-ng 11.1.0 h69a702a_8 conda-forge/linux-64 19 KB libgfortran5 11.1.0 h6c583b3_8 conda-forge/linux-64 2 MB libglib 2.68.4 h3e27bee_0 conda-forge/linux-64 3 MB libgomp 11.1.0 hc902ee8_8 conda-forge/linux-64 Cached libiconv 1.16 h516909a_0 conda-forge/linux-64 Cached liblapack 3.9.0 11_linux64_openblas conda-forge/linux-64 11 KB libllvm11 11.1.0 hf817b99_2 conda-forge/linux-64 Cached libogg 1.3.5 h27cfd23_1 pkgs/main/linux-64 199 KB libopenblas 0.3.17 pthreads_h8fe5266_1 conda-forge/linux-64 9 MB libopus 1.3.1 h7f98852_1 conda-forge/linux-64 255 KB libpng 1.6.37 hed695b0_2 conda-forge/linux-64 359 KB libpq 13.3 hd57d9b9_0 conda-forge/linux-64 3 MB libsodium 1.0.18 h516909a_1 conda-forge/linux-64 366 KB libstdcxx-ng 11.1.0 h56837e0_8 conda-forge/linux-64 Cached libtiff 4.3.0 hf544144_1 conda-forge/linux-64 668 KB libuuid 2.32.1 h14c3975_1000 conda-forge/linux-64 Cached libvorbis 1.3.7 he1b5a44_0 conda-forge/linux-64 Cached libwebp-base 1.2.1 h7f98852_0 conda-forge/linux-64 845 KB libxcb 1.14 h7b6447c_0 pkgs/main/linux-64 505 KB libxkbcommon 1.0.3 he3ba5ed_0 conda-forge/linux-64 581 KB libxml2 2.9.12 h72842e0_0 conda-forge/linux-64 772 KB livereload 2.6.3 pyh9f0ad1d_0 conda-forge/noarch 24 KB lz4-c 1.9.3 h9c3ff4c_1 conda-forge/linux-64 179 KB markdown-it-py 0.6.2 pyhd8ed1ab_0 conda-forge/noarch 55 KB markupsafe 2.0.1 py39h3811e60_0 conda-forge/linux-64 22 KB matplotlib 3.4.3 py39hf3d152e_0 conda-forge/linux-64 7 KB matplotlib-base 3.4.3 py39h2fa2bec_0 conda-forge/linux-64 7 MB matplotlib-inline 0.1.2 pyhd8ed1ab_2 conda-forge/noarch 11 KB mccabe 0.6.1 py_1 conda-forge/noarch 8 KB mdit-py-plugins 0.2.6 pyhd8ed1ab_0 conda-forge/noarch 29 KB mistune 0.8.4 py39h3811e60_1004 conda-forge/linux-64 54 KB more-itertools 8.8.0 pyhd8ed1ab_0 conda-forge/noarch 39 KB mypy_extensions 0.4.3 py39hf3d152e_3 conda-forge/linux-64 10 KB mysql-common 8.0.25 ha770c72_2 conda-forge/linux-64 2 MB mysql-libs 8.0.25 hfa10184_2 conda-forge/linux-64 2 MB myst-nb 0.12.3 pyhd8ed1ab_0 conda-forge/noarch 32 KB myst-parser 0.13.7 pyhd8ed1ab_0 conda-forge/noarch 37 KB nbclient 0.5.4 pyhd8ed1ab_0 conda-forge/noarch 60 KB nbconvert 5.6.0 py_0 conda-forge/noarch 381 KB nbdime 3.1.0 pyhd8ed1ab_0 conda-forge/noarch 4 MB nbformat 5.1.3 pyhd8ed1ab_0 conda-forge/noarch 47 KB ncurses 6.2 h58526e2_4 conda-forge/linux-64 Cached nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge/noarch 9 KB notebook 6.4.3 pyha770c72_0 conda-forge/noarch 6 MB nspr 4.30 h9c3ff4c_0 conda-forge/linux-64 233 KB nss 3.69 hb5efdd6_0 conda-forge/linux-64 2 MB numpy 1.21.2 py39hdbf815f_0 conda-forge/linux-64 6 MB olefile 0.46 pyh9f0ad1d_1 conda-forge/noarch 32 KB openjpeg 2.4.0 hb52868f_1 conda-forge/linux-64 444 KB openssl 1.1.1l h7f8727e_0 pkgs/main/linux-64 3 MB packaging 21.0 pyhd8ed1ab_0 conda-forge/noarch 35 KB pandas 1.3.2 py39hde0f152_0 conda-forge/linux-64 13 MB pandoc 2.14.2 h7f98852_0 conda-forge/linux-64 12 MB pandocfilters 1.4.3 py39h06a4308_1 pkgs/main/linux-64 14 KB parso 0.8.2 pyhd8ed1ab_0 conda-forge/noarch 68 KB pathspec 0.9.0 pyhd8ed1ab_0 conda-forge/noarch 31 KB pcre 8.45 h9c3ff4c_0 conda-forge/linux-64 253 KB pexpect 4.8.0 pyh9f0ad1d_2 conda-forge/noarch 47 KB pickleshare 0.7.5 py39hde42818_1002 conda-forge/linux-64 13 KB pillow 8.3.1 py39ha612740_0 conda-forge/linux-64 687 KB pip 21.2.4 pyhd8ed1ab_0 conda-forge/noarch 1 MB platformdirs 2.3.0 pyhd8ed1ab_0 conda-forge/noarch 14 KB pluggy 0.13.1 py39hf3d152e_4 conda-forge/linux-64 29 KB prometheus_client 0.11.0 pyhd8ed1ab_0 conda-forge/noarch 46 KB prompt-toolkit 3.0.20 pyha770c72_0 conda-forge/noarch 246 KB ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge/noarch 16 KB py 1.10.0 pyhd3deb0d_0 conda-forge/noarch 73 KB pycodestyle 2.7.0 pyhd8ed1ab_0 conda-forge/noarch 39 KB pycparser 2.20 pyh9f0ad1d_2 conda-forge/noarch 94 KB pydata-sphinx-theme 0.6.3 pyhd8ed1ab_0 conda-forge/noarch 1 MB pyflakes 2.3.1 pyhd8ed1ab_0 conda-forge/noarch 57 KB pygments 2.10.0 pyhd8ed1ab_0 conda-forge/noarch 760 KB pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge/noarch 48 KB pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge/noarch 60 KB pyqt 5.12.3 py39hf3d152e_7 conda-forge/linux-64 21 KB pyqt-impl 5.12.3 py39h0fcd23e_7 conda-forge/linux-64 6 MB pyqt5-sip 4.19.18 py39he80948d_7 conda-forge/linux-64 310 KB pyqtchart 5.12 py39h0fcd23e_7 conda-forge/linux-64 253 KB pyqtwebengine 5.12.1 py39h0fcd23e_7 conda-forge/linux-64 174 KB pyrsistent 0.18.0 py39h7f8727e_0 pkgs/main/linux-64 90 KB pysocks 1.7.1 py39hf3d152e_3 conda-forge/linux-64 28 KB pytest 6.2.5 py39hf3d152e_0 conda-forge/linux-64 433 KB pytest-cov 2.12.1 pyhd8ed1ab_0 conda-forge/noarch 21 KB pytest-flake8 1.0.7 pyhd3deb0d_0 conda-forge/noarch 10 KB pytest-forked 1.3.0 pyhd3deb0d_0 conda-forge/noarch 8 KB pytest-xdist 2.3.0 pyhd8ed1ab_0 conda-forge/noarch 31 KB python 3.9.7 h49503c6_0_cpython conda-forge/linux-64 28 MB python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch 240 KB python_abi 3.9 2_cp39 conda-forge/linux-64 4 KB pytz 2021.1 pyhd8ed1ab_0 conda-forge/noarch 239 KB pyyaml 5.4.1 py39h3811e60_1 conda-forge/linux-64 196 KB pyzmq 22.2.1 py39h37b5a0c_0 conda-forge/linux-64 506 KB qt 5.12.9 hda022c4_4 conda-forge/linux-64 100 MB readline 8.1 h46c0cb4_0 conda-forge/linux-64 295 KB regex 2021.8.28 py39h3811e60_0 conda-forge/linux-64 368 KB requests 2.26.0 pyhd8ed1ab_0 conda-forge/noarch 52 KB requests-unixsocket 0.2.0 py_0 conda-forge/noarch 14 KB ruamel_yaml 0.15.100 py39h27cfd23_0 pkgs/main/linux-64 260 KB scipy 1.7.1 py39hee8e79c_0 conda-forge/linux-64 22 MB send2trash 1.8.0 pyhd8ed1ab_0 conda-forge/noarch 17 KB setuptools 57.4.0 py39hf3d152e_0 conda-forge/linux-64 934 KB shellingham 1.4.0 pyh44b312d_0 conda-forge/noarch 11 KB six 1.16.0 pyh6c4a22f_0 conda-forge/noarch 14 KB smmap 3.0.5 pyh44b312d_0 conda-forge/noarch Cached sniffio 1.2.0 py39hf3d152e_1 conda-forge/linux-64 15 KB snowballstemmer 2.1.0 pyhd8ed1ab_0 conda-forge/noarch 57 KB soupsieve 2.2.1 pyhd3eb1b0_0 pkgs/main/noarch 32 KB sphinx 3.5.4 pyh44b312d_0 conda-forge/noarch 1 MB sphinx-autobuild 2021.3.14 pyhd8ed1ab_0 conda-forge/noarch 13 KB sphinx-book-theme 0.1.3 pyhd8ed1ab_0 conda-forge/noarch 208 KB sphinx-panels 0.6.0 pyhd8ed1ab_0 conda-forge/noarch 74 KB sphinx-togglebutton 0.2.3 pyhd3deb0d_0 conda-forge/noarch 9 KB sphinxcontrib-applehelp 1.0.2 py_0 conda-forge/noarch 28 KB sphinxcontrib-devhelp 1.0.2 py_0 conda-forge/noarch 22 KB sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge/noarch 31 KB sphinxcontrib-jsmath 1.0.1 py_0 conda-forge/noarch 7 KB sphinxcontrib-qthelp 1.0.3 py_0 conda-forge/noarch 25 KB sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_0 conda-forge/noarch 27 KB sqlalchemy 1.4.23 py39h3811e60_0 conda-forge/linux-64 2 MB sqlite 3.36.0 h9cd32fc_0 conda-forge/linux-64 1 MB terminado 0.11.1 py39hf3d152e_0 conda-forge/linux-64 27 KB testpath 0.5.0 pyhd8ed1ab_0 conda-forge/noarch 86 KB tk 8.6.11 h27826a3_1 conda-forge/linux-64 3 MB toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch 18 KB tomli 1.2.1 pyhd8ed1ab_0 conda-forge/noarch 15 KB tornado 6.1 py39h3811e60_1 conda-forge/linux-64 646 KB tqdm 4.62.2 pyhd8ed1ab_0 conda-forge/noarch 80 KB traitlets 5.1.0 pyhd8ed1ab_0 conda-forge/noarch 82 KB typed-ast 1.4.3 py39h3811e60_0 conda-forge/linux-64 213 KB typing_extensions 3.10.0.0 pyha770c72_0 conda-forge/noarch Cached tzdata 2021a he74cb21_1 conda-forge/noarch 121 KB uncertainties 3.1.6 pyhd8ed1ab_0 conda-forge/noarch 76 KB urllib3 1.26.6 pyhd8ed1ab_0 conda-forge/noarch 99 KB wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge/noarch 33 KB webencodings 0.5.1 py_1 conda-forge/noarch 12 KB websocket-client 0.58.0 py39h06a4308_4 pkgs/main/linux-64 66 KB wheel 0.37.0 pyhd8ed1ab_1 conda-forge/noarch 31 KB widgetsnbextension 3.5.1 py39hf3d152e_4 conda-forge/linux-64 2 MB xz 5.2.5 h516909a_1 conda-forge/linux-64 Cached yaml 0.2.5 h516909a_0 conda-forge/linux-64 82 KB zeromq 4.3.4 h9c3ff4c_1 conda-forge/linux-64 351 KB zipp 3.5.0 pyhd8ed1ab_0 conda-forge/noarch 12 KB zlib 1.2.11 h516909a_1010 conda-forge/linux-64 106 KB zstd 1.5.0 ha95c52a_0 conda-forge/linux-64 490 KB Summary: Install: 233 packages Total download: 323 MB ───────────────────────────────────────────────────────────────────────────────────────────────────── Finished _libgcc_mutex (00m:00s) 3 KB 17 KB/s Finished ld_impl_linux-64 (00m:00s) 667 KB 3 MB/s Finished jbig (00m:00s) 43 KB 130 KB/s Finished libffi (00m:00s) 51 KB 118 KB/s Finished libgfortran5 (00m:01s) 2 MB 5 MB/s Finished mysql-common (00m:03s) 2 MB 4 MB/s Finished libwebp-base (00m:03s) 845 KB 2 MB/s Finished zstd (00m:07s) 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scipy (01m:04s) 22 MB 1 MB/s Finished nbdime (01m:05s) 4 MB 260 KB/s Finished qt (01m:36s) 100 MB 5 MB/s __ __ __ __ / \ / \ / \ / \ / \/ \/ \/ \ ███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ \____ / / \_/ \_/ \_/ \ o \__, / _/ \_____/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝ mamba (0.13.0) supported by @QuantStack GitHub: https://github.com/mamba-org/mamba Twitter: https://twitter.com/QuantStack █████████████████████████████████████████████████████████████ Looking for: ['scipy', 'conda-forge::sphinx-panels', 'conda-forge::sphinx-autobuild', 'pandas', 'conda-forge::sphinx-book-theme', 'python=3.9', 'conda-forge::myst-nb', 'pip', "anaconda-project[version='>=0.10.1']", 'conda-forge::uncertainties', 'pytest-flake8', 'matplotlib', 'pytest-cov', 'jupytext', 'black', 'pytest-xdist', 'sphinx'] Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... Enabling notebook extension jupyter-js-widgets/extension... - Validating: OK done # # To activate this environment, use # # $ conda activate /home/user/physics-581-physics-inspired-computation/envs/phys-581 # # To deactivate an active environment, use # # $ conda deactivate Collecting mmf-setup Downloading mmf_setup-0.4.3-py3-none-any.whl (73 kB) Collecting sphinxcontrib-bibtex Downloading sphinxcontrib_bibtex-2.3.0-py3-none-any.whl (35 kB) Collecting sphinxcontrib-zopeext Downloading sphinxcontrib-zopeext-0.2.4.tar.gz (6.7 kB) Collecting tomlkit Downloading tomlkit-0.7.2-py2.py3-none-any.whl (32 kB) Requirement already satisfied: importlib-metadata in ./envs/phys-581/lib/python3.9/site-packages (from mmf-setup) (4.8.1) Requirement already satisfied: docutils>=0.8 in ./envs/phys-581/lib/python3.9/site-packages (from sphinxcontrib-bibtex) (0.16) Collecting pybtex-docutils>=1.0.0 Downloading pybtex_docutils-1.0.1-py3-none-any.whl (4.8 kB) Requirement already satisfied: Sphinx>=2.1 in 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./envs/phys-581/lib/python3.9/site-packages (from packaging->Sphinx>=2.1->sphinxcontrib-bibtex) (2.4.7) Building wheels for collected packages: sphinxcontrib-zopeext Building wheel for sphinxcontrib-zopeext (setup.py): started Building wheel for sphinxcontrib-zopeext (setup.py): finished with status 'done' Created wheel for sphinxcontrib-zopeext: filename=sphinxcontrib_zopeext-0.2.4-py3-none-any.whl size=5988 sha256=c69b6b753152973c7b6bfbe3d7f1cb188972c8bc4a56fe53ed5af92602a0da2a Stored in directory: /tmp/pip-ephem-wheel-cache-ejlglin8/wheels/36/50/14/83293d1a160781dcf9648481020f775bac6596ab55ffcba75a Successfully built sphinxcontrib-zopeext Installing collected packages: latexcodec, pybtex, zope.interface, tomlkit, pybtex-docutils, sphinxcontrib-zopeext, sphinxcontrib-bibtex, mmf-setup Successfully installed latexcodec-2.0.1 mmf-setup-0.4.3 pybtex-0.24.0 pybtex-docutils-1.0.1 sphinxcontrib-bibtex-2.3.0 sphinxcontrib-zopeext-0.2.4 tomlkit-0.7.2 zope.interface-5.4.0 The project is ready to run commands. Use `anaconda-project list-commands` to see what's available. source $ANACONDA2020/bin/activate root && CONDA_EXE=mamba anaconda-project run init # Custom command: see anaconda-project.yaml Installed kernelspec phys-581 in /home/user/.local/share/jupyter/kernels/phys-581 if ! grep -Fq 'source $ANACONDA2020/bin/activate /home/user/physics-581-physics-inspired-computation/envs/phys-581' ~/.bash_aliases; then \ echo 'source $ANACONDA2020/bin/activate /home/user/physics-581-physics-inspired-computation/envs/phys-581' >> ~/.bash_aliases; \ fi make[1]: Entering directory '/home/user/physics-581-physics-inspired-computation' find . -name ".ipynb_checkpoints" -prune -o \ -name "_ext" -prune -o \ -name "envs" -prune -o \ -name "*.ipynb" -o -name "*.md" \ -exec jupytext --sync {} + 2> >(grep -v "is not a paired notebook" 1>&2) [jupytext] Reading ./README.md in format md [jupytext] Reading ./Docs/Assignments/Assignment-1.md in format md [jupytext] Updating ./Docs/Assignments/Assignment-1.ipynb [jupytext] Updating ./Docs/Assignments/Assignment-1.md [jupytext] Reading ./Docs/Assignments/Assignment-0.md in format md [jupytext] Updating ./Docs/Assignments/Assignment-0.ipynb [jupytext] Updating ./Docs/Assignments/Assignment-0.md [jupytext] Reading ./Docs/index.md in format md [jupytext] Reading ./Docs/Syllabus.md in format md [jupytext] Reading ./Docs/Syllabus_Assignments.md in format md [jupytext] Reading ./Docs/Notes.md in format md [jupytext] Reading ./Docs/References.md in format md [jupytext] Reading ./Docs/Syllabus_Prerequisites.md in format md [WARNING] Deprecated: --atx-headers. Use --markdown-headings=atx instead. [jupytext] Reading ./Docs/CourseInfo.md in format md [jupytext] Reading ./Docs/README.md in format md [jupytext] Reading ./Docs/Assignments.md in format md [jupytext] Reading ./Docs/Links.md in format md [jupytext] Reading ./Docs/Reading.md in format md [jupytext] Reading ./Notes.md in format md make[1]: Leaving directory '/home/user/physics-581-physics-inspired-computation' real 5m14.144s user 3m4.389s sys 0m27.096s ``` Now when you log out, then reconnect to the CoCalc project, it should automatically activate the `phys-581` environment due to the line at the end of `~/.bash_aliases`: ```console MacOSX $ ssh smc581private (phys-581) ~$ type python3 python3 is /home/user/physics-581-physics-inspired-computation/envs/phys-581/bin/python3 ```
4. *(Optional)* After installing, you might like to clean up the downloaded files. This is especially important on [CoCalc] where disk space is at a premium: ```console conda clean --all -y ``` At this point you can start using the project, viewing the notebooks, running and editing code, etc. If you need additional packages, you should add them with `anaconda-project`. I recommend the following strategy. See if the package is available from the default conda repos, and install from there if it is available. If it is only available from [`conda-forge`] then explicitly install it from there, otherwise use `pip`: ```bash conda search --override-channels -c defaults sphinx conda search --override-channels -c conda-forge uncertainties anaconda-project add-packages sphinx anaconda-project add-packages conda-forge::uncertainties # Not available in defaults anaconda-project add-packages --pip mmf-setup # Only available through pip ``` Note: I am explicitly using `--override-channels`: this is crucial on CoCalc for now as the default `/ext/anaconda2020.02/.condarc` file has so many channels that `conda` will run out of memory. There are a few more things you should do if you are registered in the course: 5. [Create SSH keys](https://doc.cocalc.com/project-settings.html#ssh-keys), and add them [to your CoCalc account](https://doc.cocalc.com/account/ssh.html) and [to your GitLab account](https://docs.gitlab.com/ee/ssh/). your project with SSH, forwarding your SSH agent. 4. Create a [GitLab] account and send the username to your instructor so that they can give you access to the [Resources project]. 5. Create a [GitLab] repository for this course, and add this as a remote so that you can push your work to it. *You may make this project public or private as you prefer, but note that private projects may have more limited access to CI resources. See [GitLab pricing](https://about.gitlab.com/pricing/) for details.* ## CoCalc Setup There are a few more things that one should do if using the [CoCalc] platform. ### License [Purchase a license](https://cocalc.com/settings/licenses). A license is required to access the internet from projects, for example, to clone from [GitLab]. Students will be prompted for a term license from the course, but may use their own license. ### SSH Keys SSH keys are needed for two tasks: connecting to [GitLab] or other external servers **from** [CoCalc] to pull or push changes, and *(optional)* to directly connect **to** [CoCalc] from your computer without relying on the browser interface. To connect **from** [CoCalc], you need: 1. to be authenticated to a key on [CoCalc], and 2. to share the associated **public key** with the external resource (e.g. [GitLab]). If you want to work with the web interface, then you need to generate a key on [CoCalc], and then share the public key to [GitLab] etc. Do this in a new `Linux terminal` (use the New button on the top-left of the [CoCalc] interface): ```bash # This will generated a private key in ~/.ssh/id_ed25519 and a # public key in .ssh/id_ed25519.pub. The ed25518 type of key is # short and secure, but some older sites may need RSA or DSA keys # which you can use by changing the argument to -t ssh-keygen -t ed25519 # or -t rsa or -t dsa # Copy the public key and use this on GitLab etc. cat ~/.id_ed25519.pub ``` When you want to use this key, i.e. to clone or push to a private [GitLab] repo, you will need to first authenticate. This often happens automatically, but requires you enter your password multiple times. To avoid this, you can start a terminal (`bash`) with [`ssh-agent`](https://en.wikipedia.org/wiki/Ssh-agent) and add then `ssh-add` the key. The agent will then manage the key for you and you can push an pull multiple times *from that terminal* without re-authenticating. ```bash ssh-agent bash # Runs a new bash shell with ssh-agent ssh-add # May need to specify the key if you have several # No more passwords needed in this shell git fetch ... git push ... etc. ``` To connect **to** [CoCalc] from your computer with SSH, you will need to create a similar key *on your computer*, then copy the public version to CoCalc as described in [connecting to CoCalc with SSH](https://doc.cocalc.com/project-settings.html#ssh-keys). Also copy this public key to [GitLab] etc. If you opt to do this, you can then forward your authenticated credentials to [CoCalc] when you connect, and use those forwarded credentials instead of running `ssh-agent` as above. This can all be expressed in your `~.ssh/config` file *on your computer*. I recommend something like the following: ``` # ~/.ssh/config file on your computer ... Host cc581 User f6432a... Host cc* HostName ssh.cocalc.com ForwardAgent yes SetEnv LC_HG_USERNAME=Your Full Name SetEnv LC_GIT_USERNAME=Your Full Name SetEnv LC_GIT_USEREMAIL=your.name@example.com Host * AddressFamily inet # Force IPv4 # https://www.electricmonk.nl/log/2014/09/24/ # ssh-port-forwarding-bind-cannot-assign-requested-address/ ``` The first `Host cc581` is an [SSH alias](https://man.openbsd.org/ssh_config) that specifies the project-specific username. Find the correct value under your [CoCalc] project's [`Settings`](https://doc.cocalc.com/project-settings.html#ssh-keys) tab. The second entry is a wildcard that applies to every host that starts with `cc`. The last one is a general setting that applies for all hosts. Note that general settings must come after the more specific aliases. Alternatively, if you use the environmental variables `LC_HG_USERNAME` etc. *on your computer*, then you can just send the current values: ``` # ~/.ssh/config file on your computer ... Host cc* HostName ssh.cocalc.com ForwardAgent yes SendEnv LC_HG_USERNAME= SendEnv LC_GIT_USERNAME SendEnv LC_GIT_USEREMAIL ... ``` Once this is done, I can connect directly to a terminal on [CoCalc] by: 1. Starting the project from the web if it is not running (I don't think there is a workaround for this step. If the project is not running you will get an error like `f6432a...@ssh.cocalc.com: Permission denied (publickey).`. 2. Connect from a terminal *on your computer*: ```bash ssh cc581 ``` Because of the `~/.ssh/config` file, this is equivalent to directly typing something like ```bash ssh -A -o SendEnv=LC_HG_USERNAME ... f6432a...@ssh.cocalc.com ``` The `ForwardAgent yes` config (`-A` on the command line) will forward you your key to [CoCalc] which can then forward it to [GitLab] eschewing the need to enter your password. In this case you should add the public key *on your computer* to [GitLab] etc. *Note: on most laptops, your login manager will authenticate you to your SSH key when you login. If this does not happen, then you might need to first run `ssh-agent bash` and then `ssh-add` on your computer as we did above on CoCalc. If you find yourself needing to do this, search online to see if you can figure out how to have your login manager act as the SSH agent. For example, `Keychain Access.app` does this on my Mac OS X, `KWallet` does this on linux with KDE, etc.* ### Git Username In order to commit to your version control, you need to specify your username and email to [Git] or [Mercurial]. Typically this is done by adding appropriate entries in `~/.gitconfig` or `~/.hgrc`: ```bash # ~/.gitconfig file [user] email = your.name@example.com name = Your Full Name ... ``` ```bash # ~/.hgrc file [ui] username = Your Full Name ... ``` However, if you collaborate on [CoCalc], then this will not work well because all of your collaborators will be committing as you! Instead, we rely on the value of `LC_GIT_USERNAME` etc. which each user can set when using SSH to access the project. If you do not use SSH, you can set these directly in your project's **Settings > Custom environmental variables** section: ```json { "LC_GIT_USERNAME": "Your Full Name", "LC_GIT_USEREMAIL": "your.name@example.com", "LC_HG_USERNAME": "Your Full Name ", "LC_EDITOR": "vi", } ``` but this will have the same issue if you collaborate -- all committers who use the web interface will commit with this username/email. (Collaborators who use SSH to forward `LC_*` values will override these.) Restart your project for these to take effect. :::{Note} The reason for the `LC_` prefix is that SSH allows these variables to be sent by default -- others will be blocked and we do not have root access on [CoCalc] to change this behavior. We must then set the more appropriate variables `GIT_AUTHOR_NAME="${LC_GIT_USERNAME}"` etc. in `~/.bash_aliases`. Specifically, `make init` does the following (and more): ``` # ~/.gitconfig [user] # These are NOT set here... # email = # name = ... ``` ``` # ~/.hgrc [ui] username = $LC_HG_USERNAME ... ``` ``` # ~/.bash_aliases ... export GIT_AUTHOR_NAME="${LC_GIT_USERNAME}" export GIT_AUTHOR_EMAIL="${LC_GIT_USEREMAIL}" export GIT_COMMITTER_NAME="${LC_GIT_USERNAME}" export GIT_COMMITTER_EMAIL="${LC_GIT_USEREMAIL}" ... ``` ::: ## Docs To build the documents interactively: ```bash make doc-server ``` This will run [`sphinx-autobuild`](https://github.com/executablebooks/sphinx-autobuild) which will launch a webserver on http://127.0.0.1:8000 and rebuild the docs whenever you save a change. Here is the play-by-play for setting up the documentation. ```bash cd Docs sphinx-quickstart wget https://brand.wsu.edu/wp-content/themes/brand/images/pages/logos/wsu-signature-vertical.svg -O _static/wsu-logo.svg cp -r ../envs/default/lib/python3.9/site-packages/sphinx_book_theme/_templates/* _templates ``` I then edited the `conf.py` ```bash hg add local.bib _static/ _templates/ ``` [CoCalc]: "CoCalc: Collaborative Calculation and Data Science" [Conda]: "Conda: Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more." [GitHub CI]: "GitHub CI" [GitHub]: "GitHub" [GitLab]: "GitLab" [Git]: "Git" [Heptapod]: "Heptapod: is a community driven effort to bring Mercurial SCM support to GitLab" [Jupyter]: "Jupyter" [Jupytext]: "Jupyter Notebooks as Markdown Documents, Julia, Python or R Scripts" [LGTM]: "Continuous security analysis: A code analysis platform for finding zero-days and preventing critical vulnerabilities" [Mercurial]: "Mercurial" [Miniconda]: "Miniconda is a free minimal installer for conda." [MyST]: "MyST - Markedly Structured Text" [Read the Docs]: "Read the Docs homepage" [WSU Physics]: "WSU Physics Department" [`anaconda-project`]: "Anaconda Project: Tool for encapsulating, running, and reproducing data science projects." [`anybadge`]: "Python project for generating badges for your projects" [`conda-forge`]: "A community-led collection of recipes, build infrastructure and distributions for the conda package manager." [`genbadge`]: "Generate badges for tools that do not provide one." [`mmf-setup`]: "PyPI mmf-setup page" [`pytest`]: "pytest: helps you write better programs" [hg-git]: "The Hg-Git mercurial plugin" [WSU Courses CoCalc project]: [CoCalc Course File - Physics 581 Fall 2021]: [GitHub Mirror - Physics 581 Fall 2021]: "GitHub mirror" [GitLab Public Project - Physics 581 Fall 2021]: "GitLab public course project for Fall 2021." [GitLab Resources Project - Physics 581 Fall 2021]: "GitLab private resources course project for Fall 2021." [GitLab test coverage visualization]: [Official Course Repository]: "Official Physics 581 Repository hosted on GitLab" [Resources project]: "Private course resources repository." [Shared CoCalc Project - Physics 581 Fall 2021]: "581-2021 Shared CoCalc Project" [Shared CoCalc Project - Physics 581 Fall 2025]: "581-2025 Shared CoCalc Project" [Shared CoCalc Project]: "Shared CoCalc Project" [file an issue]: "Issues on the class GitLab project."