From d9c68abd083cec2bb730f76b219519b3b27b0153 Mon Sep 17 00:00:00 2001 From: gwbyeon Date: Fri, 24 Jan 2020 14:07:09 -0800 Subject: [PATCH 1/2] Update README.md Changes to README to specify joblib version <=0.11. Compatibility issues due to changes in joblib >= 0.12, that now uses loky as the default backend. Specifying backend="multiprocessing" in joblib function Parallel() does not entirely resolve this issue and needs to be investigated further. --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5b2385a..b44168b 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ For system-wide installation, you must have permissions and use with `sudo`. **REEFFIT** requires the following *Python* packages as dependencies, all of which can be installed through [`pip`](https://pip.pypa.io/). ```json cvxopt >= 1.1.6 -joblib >= 0.5.4 +0.11 >= joblib >= 0.5.4 matplotlib >= 1.1.1 numpy >= 1.6.1 scipy >= 0.9.0 @@ -26,6 +26,8 @@ pymc >= 2.2 rdatkit >= 1.0.4 ``` +* To use the --njobs parameter currently, joblib package version needs to be 0.11 or less. + * Note that you should have `RDATKit` installed and properly set up as well (see https://github.com/ribokit/RDATKit) * In your profile (e.g. `~/.bashrc`), include an environment variable `REEFFIT_HOME` that points to the **REEFFIT** home directory, e.g.: From b8bb4e370f9f4778c8781394890cf52d66021248 Mon Sep 17 00:00:00 2001 From: gwbyeon Date: Fri, 24 Jan 2020 17:11:07 -0800 Subject: [PATCH 2/2] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b44168b..ce1f2e7 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ For system-wide installation, you must have permissions and use with `sudo`. **REEFFIT** requires the following *Python* packages as dependencies, all of which can be installed through [`pip`](https://pip.pypa.io/). ```json -cvxopt >= 1.1.6 +cvxopt == 1.1.6 0.11 >= joblib >= 0.5.4 matplotlib >= 1.1.1 numpy >= 1.6.1 @@ -26,7 +26,7 @@ pymc >= 2.2 rdatkit >= 1.0.4 ``` -* To use the --njobs parameter currently, joblib package version needs to be 0.11 or less. +* To use the --njobs parameter currently, joblib package version needs to be 0.11 or less and cvxopt version needs to be 1.1.6 * Note that you should have `RDATKit` installed and properly set up as well (see https://github.com/ribokit/RDATKit)