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Fix checkpointing bug and improve CI stability (#4986)
Fixes #4964 Description of changes: - bugfix: checkpointing can be used more than once again - the regression was introduced by the ASE bindings - the checkpointing tests now save the checkpoint a second time - add missing include guards in the testsuite - fix Doxygen CI job
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Original file line number | Diff line number | Diff line change |
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# | ||
# Copyright (C) 2023-2024 The ESPResSo project | ||
# | ||
# This file is part of ESPResSo. | ||
# | ||
# ESPResSo is free software: you can redistribute it and/or modify | ||
# it under the terms of the GNU General Public License as published by | ||
# the Free Software Foundation, either version 3 of the License, or | ||
# (at your option) any later version. | ||
# | ||
# ESPResSo is distributed in the hope that it will be useful, | ||
# but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
# GNU General Public License for more details. | ||
# | ||
# You should have received a copy of the GNU General Public License | ||
# along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
# | ||
|
||
if(EXISTS "${BIBLIOGRAPHY}") | ||
file(READ "${BIBLIOGRAPHY}" FILE_CONTENTS) | ||
# convert unsupported LaTeX formatting commands to HTML | ||
string(REGEX REPLACE " textsuperscript ([^ ]+) " "<sup>\\1</sup> " FILE_CONTENTS "${FILE_CONTENTS}") | ||
string(REGEX REPLACE " textsubscript ([^ ]+) " "<sub>\\1</sub> " FILE_CONTENTS "${FILE_CONTENTS}") | ||
file(WRITE "${BIBLIOGRAPHY}" "${FILE_CONTENTS}") | ||
endif() |
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# | ||
# Copyright (C) 2019-2024 The ESPResSo project | ||
# | ||
# This file is part of ESPResSo. | ||
# | ||
# ESPResSo is free software: you can redistribute it and/or modify | ||
# it under the terms of the GNU General Public License as published by | ||
# the Free Software Foundation, either version 3 of the License, or | ||
# (at your option) any later version. | ||
# | ||
# ESPResSo is distributed in the hope that it will be useful, | ||
# but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
# GNU General Public License for more details. | ||
# | ||
# You should have received a copy of the GNU General Public License | ||
# along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
# | ||
|
||
file(READ "${INPUT}" FILE_CONTENTS) | ||
|
||
# transform BibTeX DOI fields into URL fields (bibliographic styles available | ||
# to Doxygen do not process the DOI field) | ||
string(REGEX REPLACE | ||
"([\r\n])[\t ]*doi *= *([\\{\"]+)(10\\.[0-9]+)" | ||
"\\1url=\\2https://doi.org/\\3" | ||
FILE_CONTENTS "${FILE_CONTENTS}") | ||
|
||
file(WRITE "${OUTPUT}" "${FILE_CONTENTS}") |
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