Update install readme #45
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arthurmloureiro
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| conda activate my_env | ||
| conda env update --name my_env --file=environment.yml --prune | ||
| ``` | ||
| and activate your environment with `conda activate [my_env/forecasting]`. | ||
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| Next install firecrown and augur. |
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The conda environment created by the previous conda env create command already includes Firecrown. Unless the Augur developers are planning to also modify Firecrown code, there is no reason to clone the Firecrown repository and then to pip-install Firecrown into the environment a second time.
For those Augur developers who do want to modify Firecrown code, it would be much better to have another YAML file to create an environment that does not contain Firecrown (but that does contain all of the things upon which Firecrown depends). That is complicated; in Firecrown we provide such an environment file.
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@marcpaterno if this is about lines 34-35: this was supposed to be an alternative for updating an env the user has, instead of creating a new one.
The Next install firecrown was there before, but I agree that it should be modified to reflect that this step is only needed if the user wants to modify firecrown. I will update the readme to reflect this, if you agree!
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@arthurmloureiro I agree with removing the instructions to clone Firecrown and then pip-install it. But I was also pointing out that if someone working with Augur does want to modify Firecrown code, they should not also have Firecrown (with an older version) already installed in the conda environment into which the new pip-install will be done. It can be quite tricky to make sure that such an environment has consistent versions of everything to work together correctly.
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@marcpaterno I pointed to the developer installation instructions from Firecrown :)
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CI is breaking because of this: Scipy changed the namespace from |
In Firecrown we encountered failures in a library being called from CCL that was not yet consistent with the SciPy 1.14 release. We handled the problem by putting a requirement of scipy < 1.14 into Firecrown's environment.yml. The same may work for Augur. |
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This PR also fixes issues with the cosmosis example. |
Updates the installation instructions in the readme file to create/update environments with the dependencies.
Following the current instructions resulted in missing dependencies such as TJPCov.
It also fixes the cosmosis examples that needed updating.