From 4c780cb495752e8b8c00af80e5f56667d467108a Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 11:04:12 +0200 Subject: [PATCH 1/8] Minor changes to installation instructions --- docs/getting_started.rst | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/getting_started.rst b/docs/getting_started.rst index 14c2168..d2b90b6 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -9,6 +9,9 @@ LePHARE is distributed with `pypi `_, and thu .. code-block:: bash + # We recommend using Python 3.12 which is the best tested + conda create -n python=3.12 + conda activate pip install lephare .. note:: @@ -131,7 +134,7 @@ editable mode with the `-e` option so that any changes are immediately propagate .. code-block:: bash - conda create env -n + conda create -n python=3.12 conda activate conda install cxx-compilers # May not be required for linux git clone https://github.com/lephare-photoz/lephare.git @@ -144,7 +147,7 @@ editable mode with the `-e` option so that any changes are immediately propagate .. code-block:: bash - conda create env -n + conda create -n python=3.12 conda activate conda install cxx-compilers brew install llvm libomp From db7cfaa665ad8bfa2949f45701230b02e3c446fc Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 11:20:57 +0200 Subject: [PATCH 2/8] Attempt to fix cppp coverage issue --- src/lib/_bindings.cc | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/lib/_bindings.cc b/src/lib/_bindings.cc index 79a9d59..c805c73 100644 --- a/src/lib/_bindings.cc +++ b/src/lib/_bindings.cc @@ -63,10 +63,9 @@ PYBIND11_MODULE(_lephare, mod) { "standard constructor") .def_readwrite("lamb_opa", &opa::lamb_opa) .def_readwrite("opared", &opa::red) - .def("read", &opa::read) - // .def("lmin", &opa::lmin, "return smallest wavelength stored") - // .def("lmax", &opa::lmax, "return largest wavelength stored") - ; + .def("read", &opa::read); + // .def("lmin", &opa::lmin, "return smallest wavelength stored") + // .def("lmax", &opa::lmax, "return largest wavelength stored") /******** CLASS EXT *********/ py::class_(mod, "ext") From 42a7e8fc815262108a7b1705b9f66d1c18858cf7 Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 11:25:41 +0200 Subject: [PATCH 3/8] Attempting to fix code coverage error --- .github/workflows/testing-and-coverage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing-and-coverage.yml b/.github/workflows/testing-and-coverage.yml index 17df281..5b186b8 100644 --- a/.github/workflows/testing-and-coverage.yml +++ b/.github/workflows/testing-and-coverage.yml @@ -43,7 +43,7 @@ jobs: - name: Collect C++ coverage run: | - lcov --output-file coverage.cpp --capture --directory build + lcov --output-file coverage.cpp --capture --directory build --rc geninfo_ignore_errors=mismatch lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" cat coverage.lcov coverage.cpp > coverage.txt From 77df555dfe9fdd475a93affad012df2998bf9787 Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 11:30:36 +0200 Subject: [PATCH 4/8] Attempting to fix code coverage error with additional line --- .github/workflows/testing-and-coverage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing-and-coverage.yml b/.github/workflows/testing-and-coverage.yml index 5b186b8..1578150 100644 --- a/.github/workflows/testing-and-coverage.yml +++ b/.github/workflows/testing-and-coverage.yml @@ -44,7 +44,7 @@ jobs: - name: Collect C++ coverage run: | lcov --output-file coverage.cpp --capture --directory build --rc geninfo_ignore_errors=mismatch - lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" + lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" --rc geninfo_ignore_errors=mismatch cat coverage.lcov coverage.cpp > coverage.txt - name: Upload coverage report to codecov From ce34fd187f8377685fdb8a239045e991d86155db Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 12:54:11 +0200 Subject: [PATCH 5/8] revert testing test --- .github/workflows/testing-and-coverage.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/testing-and-coverage.yml b/.github/workflows/testing-and-coverage.yml index 1578150..17df281 100644 --- a/.github/workflows/testing-and-coverage.yml +++ b/.github/workflows/testing-and-coverage.yml @@ -43,8 +43,8 @@ jobs: - name: Collect C++ coverage run: | - lcov --output-file coverage.cpp --capture --directory build --rc geninfo_ignore_errors=mismatch - lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" --rc geninfo_ignore_errors=mismatch + lcov --output-file coverage.cpp --capture --directory build + lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" cat coverage.lcov coverage.cpp > coverage.txt - name: Upload coverage report to codecov From ea8c2e50f1afa7b224dfe64eb48bb61250801e31 Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 13:35:23 +0200 Subject: [PATCH 6/8] Further attempt to fix coverage error --- .github/workflows/testing-and-coverage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing-and-coverage.yml b/.github/workflows/testing-and-coverage.yml index 17df281..fdc4711 100644 --- a/.github/workflows/testing-and-coverage.yml +++ b/.github/workflows/testing-and-coverage.yml @@ -43,7 +43,7 @@ jobs: - name: Collect C++ coverage run: | - lcov --output-file coverage.cpp --capture --directory build + lcov --output-file coverage.cpp --capture --directory build --rc geninfo_unexecuted_blocks=1 --ignore-errors mismatch,gcov,gcov lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" cat coverage.lcov coverage.cpp > coverage.txt From 6195c88cb817734cab3762f19e5ca4797ba2c5a1 Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Tue, 15 Oct 2024 13:44:22 +0200 Subject: [PATCH 7/8] Moving lcov stuff to other branch --- .github/workflows/testing-and-coverage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing-and-coverage.yml b/.github/workflows/testing-and-coverage.yml index fdc4711..17df281 100644 --- a/.github/workflows/testing-and-coverage.yml +++ b/.github/workflows/testing-and-coverage.yml @@ -43,7 +43,7 @@ jobs: - name: Collect C++ coverage run: | - lcov --output-file coverage.cpp --capture --directory build --rc geninfo_unexecuted_blocks=1 --ignore-errors mismatch,gcov,gcov + lcov --output-file coverage.cpp --capture --directory build lcov --output-file coverage.cpp --extract coverage.cpp $PWD/src/"*" cat coverage.lcov coverage.cpp > coverage.txt From 48b227744d3e4949acd19803e3ef8e1016ee22e9 Mon Sep 17 00:00:00 2001 From: Raphael Shirley Date: Wed, 16 Oct 2024 15:03:22 +0200 Subject: [PATCH 8/8] Remove unnecesary installation line There was a repeated line with a typo which did not do anything so I removed it. --- docs/getting_started.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/getting_started.rst b/docs/getting_started.rst index d2b90b6..def9dbf 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -136,7 +136,6 @@ editable mode with the `-e` option so that any changes are immediately propagate conda create -n python=3.12 conda activate - conda install cxx-compilers # May not be required for linux git clone https://github.com/lephare-photoz/lephare.git cd lephare git submodule update --init --recursive @@ -149,7 +148,6 @@ editable mode with the `-e` option so that any changes are immediately propagate conda create -n python=3.12 conda activate - conda install cxx-compilers brew install llvm libomp git clone https://github.com/lephare-photoz/lephare.git cd lephare