User local installation documentation and bash script #418
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Created two files (`local-installation.md` and `local_install_or_update.sh`) that will likely make it easier for new flepiMoP users to install flepiMoP onto their machine.
TimothyWillard
requested changes
Dec 12, 2024
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Great start! I left comments mostly on the docs rather than the script since I think the script will be easier to tackle after docs are clear and can run the script after fixing the first major bug. My big picture comments are:
- Let's merge this int
devinstead ofmainto be consistent with the new development workflow. - We need to be clear that this install script is for Mac/Linux users and we will need to add a windows equivalent or steps for windows users but that's not your responsibility @emprzy. We'll find and work with a windows user who can test that part.
- I think it's worth pointing out somewhere why we recommend
condaand use that as our default installation. I think there is resistance tocondasince it adds an extra layer for users and we want to make clear why it's worth jumping that hurdle.
TimothyWillard
added
documentation
TimothyWillard
requested changes
Dec 20, 2024
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I get this error:
twillard@epid-iss-MacBook-Pro ~/D/G/H/flepiMoP ((cbecd91c))> ./build/local_install_or_update
Using '/Users/twillard/Desktop/GitHub/HopkinsIDD/flepiMoP' for $FLEPI_PATH.
Using 'flepimop-env' for $FLEPI_CONDA.
CondaError: Run 'conda init' before 'conda activate'
I think due to the wrong ordering for conda setup mentioned inline.
build/local_install_or_update
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| # Create the conda environment if it doesn't exist | ||
| if ! conda env list | grep -q "$FLEPI_CONDA"; then | ||
| conda env create --name flepimop-env --file $FLEPI_PATH/environment.yml | ||
| fi | ||
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| # Ensure that conda environment is named flepimop-env | ||
| if [ -z "${FLEPI_CONDA}" ]; then | ||
| export FLEPI_CONDA="flepimop-env" | ||
| echo "Using '$FLEPI_CONDA' for \$FLEPI_CONDA." | ||
| fi | ||
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| # Activate the conda environment | ||
| conda activate $FLEPI_CONDA | ||
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| # Check that the name of the FLEPI_CONDA variable matches the environment that has been set up, exit if not | ||
| FLEPI_CONDA_ENV_MATCHES=$( conda info --envs | awk '{print $1}' | grep -x "$FLEPI_CONDA" | wc -l ) | ||
| if [ "$FLEPI_CONDA_ENV_MATCHES" -eq 0 ]; then | ||
| echo "Issue with conda environment: ensure you have set up your conda environment and it has the correct name." | ||
| exit 1 | ||
| fi | ||
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| # Load the conda environment | ||
| eval "$(conda shell.bash hook)" | ||
| conda activate $FLEPI_CONDA |
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This seems to be in the wrong order/have the wrong logic. The
conda env create --name flepimop-env --file $FLEPI_PATH/environment.ymlshould be in side of the
if [ "$FLEPI_CONDA_ENV_MATCHES" -eq 0 ]; then
.....
fiblock? And then there shouldn't be two calls to conda activate right? I think we want the created env to have the name pulled from $FLEPI_CONDA right?
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Okay I re-downloaded conda then tested the script (with changes) locally. Everything seems to work. I think there were issues with my conda environment but it should be working correctly now. Ready again for a test on your end
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Describe your changes.
This pull request creates a new section of documentation (in a file called
local-installation.md) that delineates more up-to-date installation instructions for new flepiMoP users. Within these instructions, users are instructed to run a bash script (also created in this PR:local_install_or_update.sh). This script:FLEPI_PATHto be equal to the current working directory and tests that this is the right directory (exits on fail with message)condaenvironment is set up correctly and aligns with demands of flepiMoP (exits on fail with message)gempyor+ dependencies and all R packages + dependenciesImportant note: The existence
local-installation.mddocumentation page renders some information on other documentation pages redundant or outdated, so I will need to go back and adjust accordingly after I get a thumbs up on the general structure of these two files! @TimothyWillardDoes this pull request make any user interface changes? If so please describe.
The user interface changes are slightly altered local installation instructions for flepiMoP.
Those are reflected in updates to the documentation in
local-installation.md.What does your pull request address? Tag relevant issues.
This pull request addresses GH #401 .