From f6a536a22203eabd9de66d9564e5834f94252ce4 Mon Sep 17 00:00:00 2001 From: jajupmochi Date: Mon, 19 Oct 2020 15:20:18 +0200 Subject: [PATCH 1/4] Remove the tests on Python 3.9. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index a99fedb..217221a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,7 +4,6 @@ python: - '3.6' - '3.7' - '3.8' -- '3.9' before_install: - python --version @@ -13,6 +12,7 @@ before_install: - pip install codecov - pip install coverage - pip install pytest-cov +- sudo apt-get -y install gfortran install: - pip install -r requirements.txt From 8a583296c4d4ffbb0b4436f71bddeae94570e8e6 Mon Sep 17 00:00:00 2001 From: jajupmochi Date: Mon, 19 Oct 2020 15:29:30 +0200 Subject: [PATCH 2/4] Test slycot. --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 2e8cbc0..43b0f5e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ scikit-learn>=0.20.0 tabulate>=0.8.2 tqdm>=4.26.0 control>=0.8.2 # for generalized random walk kernels only. -slycot>=0.4.0 # for generalized random walk kernels only, which requires a fortran compiler, gfortran for example +slycot>=0.3.3 # for generalized random walk kernels only, which requires a fortran compiler, gfortran for example cvxpy>=1.0.31 # for preimage. Does not work for "pip install graphkit-learn". # -e https://files.pythonhosted.org/packages/11/d0/d900870dc2d02ea74961b90c353666c6528a33ea61a10aa59a0d5574ae59/cvxpy-1.0.31.tar.gz # for preimage. cvxopt>=1.2.5 # for preimage. From 02708e0f497b48e4c3b0cb02226e6b578227d156 Mon Sep 17 00:00:00 2001 From: jajupmochi Date: Mon, 19 Oct 2020 15:54:34 +0200 Subject: [PATCH 3/4] Test slycot. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 217221a..b40cbcb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,7 @@ before_install: - pip install codecov - pip install coverage - pip install pytest-cov -- sudo apt-get -y install gfortran +- sudo apt-get -y install gfortran liblapack-dev install: - pip install -r requirements.txt From 993e8f591d1f512ec4796aeea2a6c02cfb8abfec Mon Sep 17 00:00:00 2001 From: jajupmochi Date: Mon, 19 Oct 2020 16:22:47 +0200 Subject: [PATCH 4/4] Fix bugs when installing slycot. --- Problems.md | 5 +++++ README.md | 2 +- requirements.txt | 2 +- requirements_pypi.txt | 2 +- 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/Problems.md b/Problems.md index cb7dd1e..852726a 100644 --- a/Problems.md +++ b/Problems.md @@ -21,3 +21,8 @@ export LD_LIBRARY_PATH=/opt/intel/lib/intel64:/opt/intel/mkl/lib/intel64:$LD_LIB export LD_PRELOAD=/opt/intel/mkl/lib/intel64/libmkl_def.so:/opt/intel/mkl/lib/intel64/libmkl_avx2.so:/opt/intel/mkl/lib/intel64/libmkl_core.so:/opt/intel/mkl/lib/intel64/libmkl_intel_lp64.so:/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so:/opt/intel/lib/intel64_lin/libiomp5.so ``` + +### Module `slycot` install error. + +A fortran compiler (e.g., `gfortran`) and BLAS/LAPACK (e.g. `liblapack-dev`) needs to be pre-installed. Try to include them in the library or remove these dependences. See [slycot's file](https://github.com/python-control/Slycot/blob/master/.travis.yml) for detail. + diff --git a/README.md b/README.md index a8720cf..91215c8 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ A Python package for graph kernels, graph edit distances and graph pre-image pro * tabulate>=0.8.2 * tqdm>=4.26.0 * control>=0.8.2 (for generalized random walk kernels only) -* slycot>0.4.0 (for generalized random walk kernels only, which requires a fortran compiler, gfortran for example) +* slycot>=0.3.3 (for generalized random walk kernels only, which requires a fortran compiler (e.g., `gfortran`) and BLAS/LAPACK (e.g. `liblapack-dev`)) ## How to use? diff --git a/requirements.txt b/requirements.txt index 43b0f5e..4b25bb3 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ scikit-learn>=0.20.0 tabulate>=0.8.2 tqdm>=4.26.0 control>=0.8.2 # for generalized random walk kernels only. -slycot>=0.3.3 # for generalized random walk kernels only, which requires a fortran compiler, gfortran for example +slycot>=0.3.3 # for generalized random walk kernels only, which requires a fortran compiler (e.g., `gfortran`) and BLAS/LAPACK (e.g. `liblapack-dev`) cvxpy>=1.0.31 # for preimage. Does not work for "pip install graphkit-learn". # -e https://files.pythonhosted.org/packages/11/d0/d900870dc2d02ea74961b90c353666c6528a33ea61a10aa59a0d5574ae59/cvxpy-1.0.31.tar.gz # for preimage. cvxopt>=1.2.5 # for preimage. diff --git a/requirements_pypi.txt b/requirements_pypi.txt index 1a42146..3c68618 100644 --- a/requirements_pypi.txt +++ b/requirements_pypi.txt @@ -6,7 +6,7 @@ scikit-learn>=0.20.0 tabulate>=0.8.2 tqdm>=4.26.0 control>=0.8.2 # for generalized random walk kernels only. -# slycot>=0.4.0 # for generalized random walk kernels only, which requires a fortran compiler, gfortran for example +# slycot>=0.3.3 # for generalized random walk kernels only, which requires a fortran compiler (e.g., `gfortran`) and BLAS/LAPACK (e.g. `liblapack-dev`) # cvxpy>=1.0.31 # for preimage. Does not work for "pip install graphkit-learn". # -e https://files.pythonhosted.org/packages/11/d0/d900870dc2d02ea74961b90c353666c6528a33ea61a10aa59a0d5574ae59/cvxpy-1.0.31.tar.gz # for preimage. cvxopt>=1.2.5 # for preimage.