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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -116,12 +116,36 @@ jobs: | |
| - name: Checkout website repository | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| ssh-key: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }} | ||
| repository: 'Colvars/colvars.github.io' | ||
| path: 'website' | ||
|
|
||
| - name: Build doc | ||
| - name: Build doc for current branch | ||
| working-directory: doc | ||
| run: apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make | ||
| run: | | ||
| make clean-all | ||
| apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make | ||
| - name: Install SSH key for access to website repository | ||
| if: contains(github.event.head_commit.message, '[update-doc]') | ||
| env: | ||
| WEBSITE_SSH_KEY: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }} | ||
| run: | | ||
| mkdir -p -m 700 ~/.ssh | ||
| echo "${WEBSITE_SSH_KEY}" > ~/.ssh/website | ||
| chmod 600 ~/.ssh/website | ||
| - name: Push updated doc to website repository | ||
| working-directory: doc | ||
| if: contains(github.event.head_commit.message, '[update-doc]') | ||
| env: | ||
| COLVARS_WEBSITE_TREE: ${{ github.workspace }}/website | ||
| run: | | ||
| apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make install | ||
| export GIT_SSH="ssh -i ~/.ssh/website" | ||
| git config --global user.email "[email protected]" | ||
| git config --global user.name "CI runner" | ||
| bash update_website.sh ${{ github.workspace }}/website | ||
| codeql: | ||
|
|
@@ -222,10 +246,6 @@ jobs: | |
| key: ${{ runner.os }}-build-asan-${{ github.sha }} | ||
| restore-keys: ${{ runner.os }}-build-asan- | ||
|
|
||
| - name: Install build dependencies for library | ||
| run: | | ||
| sudo apt -y install tcl8.6-dev clang-14 clang-tools-14 | ||
| - name: Checkout OpenMM (for Lepton library) | ||
| uses: actions/checkout@v4 | ||
| with: | ||
|
|
@@ -406,6 +426,17 @@ jobs: | |
| scl enable gcc-toolset-12 -- \ | ||
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | ||
| - name: GCC 13, C++20 (CentOS 9) | ||
| env: | ||
| CXX_STANDARD: 20 | ||
| CXX: g++ | ||
| CXX_VERSION: 13 | ||
| CC: gcc | ||
| run: | | ||
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | ||
| scl enable gcc-toolset-13 -- \ | ||
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | ||
| - name: Clang 16, C++11 (CentOS 9) | ||
| env: | ||
| CXX_STANDARD: 11 | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -3,7 +3,7 @@ | |
| # Invoke this script with --help for documentation. | ||
|
|
||
| # Download link: https://github.com/Colvars/colvars/blob/master/colvartools/plot_colvars_traj.py?raw=true | ||
| # This version was modified on: 2023-07-13 | ||
| # This version was modified on: 2024-01-16 | ||
| # Contact: [email protected] | ||
|
|
||
| from __future__ import print_function | ||
|
|
@@ -314,10 +314,10 @@ def as_pandas(self, keys=None): | |
|
|
||
| parser.add_argument('--output-file', | ||
| type=str, | ||
| help='Write the selected variables to a text file. ' | ||
| 'The step number is always included as the first ' | ||
| 'column, and all variables ' | ||
| 'must be defined on the same trajectory segments.', | ||
| help="Write the selected variables to a file in NumPy format " | ||
| " (if the extension is .npz) or in text format otherwise. " | ||
| "The step number is included as the first column, and all variables " | ||
| "must be defined on the same trajectory segments.", | ||
| default=None) | ||
|
|
||
| parser.add_argument('--plot-file', | ||
|
|
@@ -388,24 +388,36 @@ def as_pandas(self, keys=None): | |
| plot_keys = dict(zip(variables, variables)) | ||
|
|
||
|
|
||
| if (args.output_file): | ||
| if args.output_file: | ||
|
|
||
| fmt = " %12d" | ||
| columns = [colvars_traj[variables[0]].steps] | ||
| output_file = args.output_file | ||
| numpy_format = False | ||
| if output_file.endswith(".npz"): | ||
| numpy_format = True | ||
| if output_file == '-': | ||
| output_file = sys.stdout | ||
|
|
||
| text_fmt_string = " %12d" | ||
| if numpy_format: | ||
| columns = { 'step' : colvars_traj[variables[0]].steps } | ||
| else: | ||
| columns = [colvars_traj[variables[0]].steps] | ||
| for var in variables: | ||
| cv = colvars_traj[var] | ||
| for ic in range(cv.num_dimensions): | ||
| y = cv.values | ||
| if (cv.num_dimensions > 1): | ||
| if cv.num_dimensions > 1 and not numpy_format: | ||
| y = cv.values[:,ic] | ||
| columns += [y] | ||
| fmt += " %21.14f" | ||
| columns = tuple(columns) | ||
| output_file = args.output_file | ||
| if (output_file == '-'): output_file = sys.stdout | ||
| np.savetxt(fname=output_file, | ||
| X=list(zip(*columns)), | ||
| fmt=str(fmt)) | ||
| if numpy_format: | ||
| columns[var] = y | ||
| else: | ||
| columns += [y] | ||
| text_fmt_string += " %21.14f" | ||
|
|
||
| if numpy_format: | ||
| np.savez(output_file, **columns) | ||
| else: | ||
| np.savetxt(fname=output_file, X=np.column_stack(columns), fmt=str(text_fmt_string)) | ||
|
|
||
| else: | ||
|
|
||
|
|
||
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