diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..5391d87392a9983b4dcac6751022ac8b0c20e424
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,138 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# For a library or package, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d7cebebe071ca4f19a60bab63fc80e67e77a5e7d..a0a1fbea929928df1eb4357b906fb112d2583cf4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,49 +1,55 @@
+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration #
+# #
+# This software is distributed under the terms of the GNU General Public #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING". #
+# #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization #
+# or submit itself to any jurisdiction. #
+###############################################################################
image: python:latest
-# Change pip's cache directory to be inside the project directory since we can
-# only cache local items.
-variables:
- PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+pre-commit:
+ stage: build
+ before_script:
+ - pip install pre-commit
+ script:
+ - pre-commit run --all-files
+ variables:
+ PRE_COMMIT_HOME: ${CI_PROJECT_DIR}/.cache/pre-commit
+ cache:
+ paths:
+ - ${PRE_COMMIT_HOME}
-# Pip's cache doesn't store the python packages
-# https://pip.pypa.io/en/stable/topics/caching/
-#
-# If you want to also cache the installed packages, you have to install
-# them in a virtualenv and cache it as well.
-cache:
- paths:
- - .cache/pip
- - venv/
-build-env:
- stage: build
- script:
+.setup_environment:
+ before_script:
- python --version ; pip --version # For debugging
- pip install virtualenv
- virtualenv venv
- source venv/bin/activate
- - pip install numpy
+ - pip install .
+
extract-and-convert-table-2018-050:
+ extends: .setup_environment
stage: test
script:
- - source venv/bin/activate
- - python extract_tables_from_source.py -f "TestAnalyses/LHCb-PAPER-2018-050/bfrac-13.tex"
- - python extract_tables_from_source.py -f "TestAnalyses/LHCb-PAPER-2018-050/Supplementary.tex"
- - python tex_to_yaml.py --file "ptB.tex" --format "i d stat sys d stat sys"
+ - gethepdata extract_tables -f "TestAnalyses/LHCb-PAPER-2018-050/bfrac-13.tex"
+ - gethepdata extract_tables -f "TestAnalyses/LHCb-PAPER-2018-050/Supplementary.tex"
+ - gethepdata tex_to_yaml --file "ptB.tex" --format "i d stat sys d stat sys"
- ls *.yaml | grep "ptB.yaml"
- needs: ["build-env"]
artifacts:
when: always
extract-and-convert-table-2020-018:
+ extends: .setup_environment
stage: test
- needs: ["build-env"]
script:
- - source venv/bin/activate
- - python extract_tables_from_source.py -f "TestAnalyses/LHCb-PAPER-2020-018/main.tex"
- - python tex_to_yaml.py --file eta_results.tex --format "i d e d e d e"
+ - gethepdata extract_tables -f "TestAnalyses/LHCb-PAPER-2020-018/main.tex"
+ - gethepdata tex_to_yaml --file eta_results.tex --format "i d e d e d e"
- ls *.yaml | grep "eta_results.yaml"
artifacts:
when: always
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fed67d9ecf6e7668caef55d7ed10a72e3088d1bc
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,12 @@
+repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.5.0
+ hooks:
+ - id: check-added-large-files
+ - id: no-commit-to-branch
+ args: [--branch, main]
+
+ - repo: https://gitlab.cern.ch/lhcb-core/LbDevTools
+ rev: 2.0.40
+ hooks:
+ - id: lb-add-copyright
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000000000000000000000000000000000000..f288702d2fa16d3cdf0035b15a9fcbc552cd88e7
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights. Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received. You must make sure that they, too, receive
+or can get the source code. And you must show them these terms so they
+know their rights.
+
+ Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+ For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software. For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+ Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so. This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software. The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable. Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products. If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+ Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary. To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+ "The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.
+
+ To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy. The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+ A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+ To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+ To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+ An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License. If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+ 1. Source Code.
+
+ The "source code" for a work means the preferred form of the work
+for making modifications to it. "Object code" means any non-source
+form of a work.
+
+ A "Standard Interface" means an interface that either is an official
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+ The "System Libraries" of an executable work include anything, other
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+implementation is available to the public in source code form. A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+ The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
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+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+ The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.
+
+ The Corresponding Source for a work in source code form is that
+same work.
+
+ 2. Basic Permissions.
+
+ All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+ You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force. You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright. Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+
+ Conveying under any other circumstances is permitted solely under
+the conditions stated below. Sublicensing is not allowed; section 10
+makes it unnecessary.
+
+ 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+ No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
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+
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+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+
+ 4. Conveying Verbatim Copies.
+
+ You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+ You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
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+ 5. Conveying Modified Source Versions.
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+ You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+
+ a) The work must carry prominent notices stating that you modified
+ it, and giving a relevant date.
+
+ b) The work must carry prominent notices stating that it is
+ released under this License and any conditions added under section
+ 7. This requirement modifies the requirement in section 4 to
+ "keep intact all notices".
+
+ c) You must license the entire work, as a whole, under this
+ License to anyone who comes into possession of a copy. This
+ License will therefore apply, along with any applicable section 7
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+ invalidate such permission if you have separately received it.
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+ interfaces that do not display Appropriate Legal Notices, your
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+works, which are not by their nature extensions of the covered work,
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+in or on a volume of a storage or distribution medium, is called an
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+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
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+ You may convey a covered work in object code form under the terms
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+ written offer, valid for at least three years and valid for as
+ long as you offer spare parts or customer support for that product
+ model, to give anyone who possesses the object code either (1) a
+ copy of the Corresponding Source for all the software in the
+ product that is covered by this License, on a durable physical
+ medium customarily used for software interchange, for a price no
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+ only if you received the object code with such an offer, in accord
+ with subsection 6b.
+
+ d) Convey the object code by offering access from a designated
+ place (gratis or for a charge), and offer equivalent access to the
+ Corresponding Source in the same way through the same place at no
+ further charge. You need not require recipients to copy the
+ Corresponding Source along with the object code. If the place to
+ copy the object code is a network server, the Corresponding Source
+ may be on a different server (operated by you or a third party)
+ that supports equivalent copying facilities, provided you maintain
+ clear directions next to the object code saying where to find the
+ Corresponding Source. Regardless of what server hosts the
+ Corresponding Source, you remain obligated to ensure that it is
+ available for as long as needed to satisfy these requirements.
+
+ e) Convey the object code using peer-to-peer transmission, provided
+ you inform other peers where the object code and Corresponding
+ Source of the work are being offered to the general public at no
+ charge under subsection 6d.
+
+ A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+
+ A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling. In determining whether a product is a consumer product,
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+typical or common use of that class of product, regardless of the status
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+ "Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source. The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.
+
+ If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information. But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).
+
+ The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
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+the User Product in which it has been modified or installed. Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.
+
+ Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.
+
+ 7. Additional Terms.
+
+ "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.
+
+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the
+ terms of sections 15 and 16 of this License; or
+
+ b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or
+
+ c) Prohibiting misrepresentation of the origin of that material, or
+ requiring that modified versions of such material be marked in
+ reasonable ways as different from the original version; or
+
+ d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or
+
+ e) Declining to grant rights under trademark law for use of some
+ trade names, trademarks, or service marks; or
+
+ f) Requiring indemnification of licensors and authors of that
+ material by anyone who conveys the material (or modified versions of
+ it) with contractual assumptions of liability to the recipient, for
+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.
+
+ All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+
+ If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
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+ Nothing in this License shall be construed as excluding or limiting
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+
+ 12. No Surrender of Others' Freedom.
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+
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+copy of the Program in return for a fee.
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+
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+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
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+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
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+ it under the terms of the GNU General Public License as published by
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+ (at your option) any later version.
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+ This program 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 <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
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+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/README.md b/README.md
index 6204d626587467f2455714c8bb6df05a84d9acd2..2e462b965a28e47e9b3039cd3ab8a4b63764ab19 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# HepDataExtractor
-Simple python scripts to extract tables from LaTeX papers and convert them to HepData entries
+Simple python tool to extract tables from LaTeX papers and convert them to HepData entries
## Helping to Develop
@@ -12,37 +12,37 @@ Spotted an error? Need something special you think is useable by others? Create
### I have a LaTeX file with just the tables I want to process
-In some ways this is the easiest way to do things! You can simply pass the file to `tex_to_yaml.py` via the command line, e.g.
+In some ways this is the easiest way to do things! You can simply pass the file to `tex_to_yaml` via the command line, e.g.
```
-python tex_to_yaml.py --file myfile.tex --format "i d stat syst d stat syst"
+gethepdata tex_to_yaml --file myfile.tex --format "i d stat syst d stat syst"
```
if you need help with the command line documents, type
```
-python tex_to_yaml.py --help
+gethepdata tex_to_yaml --help
```
### I have a document which I want to process the tables for
-Not a problem! The script `extract_tables_from_source.py` extracts all the tables from a document (including recursively by passing only the `main.tex` file). You can call from the command line using
+Not a problem! The command `extract_tables` extracts all the tables from a document (including recursively by passing only the `main.tex` file). You can call from the command line using
```
-python extract_tables_from_source.py --file /path/to/main.tex
+gethepdata extract_tables --file /path/to/main.tex
```
-which will then use the `\label` argument to determine the tex file name.
+which will then use the `\label` argument to determine the `.tex` file name.
### My submission is ready! Create the `submission.yaml` file
-Once you have all tables in the `.yaml` format, you can run the script `make_submission_yaml_file.py` to create the relevant file suitable for hepdata submission
+Once you have all tables in the `.yaml` format, you can run the command `prepare_submission` to create the relevant file suitable for HepData submission
```
-python make_submission_yaml_file.py --files *.yaml
+gethepdata prepare_submission --files *.yaml
```
-This will create the `submission.yaml` based on the *.yaml files produced by the `tex_to_yaml.py` step.
+This will create the `submission.yaml` based on the output of the `tex_to_yaml` step.
-Original Author: Harvey Turner, Manchester, supervised by Adam Davis and Will Barter. Updated 11 August 2023 by Adam Davis
\ No newline at end of file
+Original Author: Harvey Turner, Manchester, supervised by Adam Davis and Will Barter. Updated 11 August 2023 by Adam Davis
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000000000000000000000000000000000..aadc8d6c1b91148ec939ddf30a5aebdeb0e3fcb9
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
+[project]
+name = "HepDataExtractor"
+dependencies = [
+ "pyyaml",
+ "numpy"
+]
+dynamic = ["version"]
+description = "Simple python tool to extract tables from LaTeX papers and convert them to HepData entries"
+authors = [
+ {name = "Adam Davis"},
+ {name = "Harvey Turner"},
+ {name = "Will Barter"}
+]
+maintainers = [
+ {name = "LHCb Simulation"}
+]
+readme = "README.md"
+classifiers = [
+ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+ "Programming Language :: Python :: 3"
+]
+
+[project.urls]
+Repository = "https://gitlab.cern.ch/lhcb-simulation/hepdataextractor"
+"Bug Tracker" = "https://gitlab.cern.ch/lhcb-simulation/hepdataextractor/-/issues"
+
+[project.scripts]
+gethepdata = "HepDataExtractor.__main__:parse_args"
diff --git a/src/HepDataExtractor/__init__.py b/src/HepDataExtractor/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..713e41d682f6125f41e0fbe2d4c0b3141dc2231c
--- /dev/null
+++ b/src/HepDataExtractor/__init__.py
@@ -0,0 +1,10 @@
+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration #
+# #
+# This software is distributed under the terms of the GNU General Public #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING". #
+# #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization #
+# or submit itself to any jurisdiction. #
+###############################################################################
diff --git a/src/HepDataExtractor/__main__.py b/src/HepDataExtractor/__main__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5102afb2cebb43683289a5c4bd734d272e4f1a08
--- /dev/null
+++ b/src/HepDataExtractor/__main__.py
@@ -0,0 +1,49 @@
+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration #
+# #
+# This software is distributed under the terms of the GNU General Public #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING". #
+# #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization #
+# or submit itself to any jurisdiction. #
+###############################################################################
+import argparse
+
+from .extract_tables_from_source import main as etfs
+from .make_submission_yaml_file import main as msyf
+from .tex_to_yaml import main as tty
+
+def parse_args():
+ parser = argparse.ArgumentParser()
+ subparsers = parser.add_subparsers(dest="action", required=True)
+
+ # extract_tables_from_source
+ etfs_parser = subparsers.add_parser("extract_tables")
+ etfs_parser.add_argument('-f','--file',type=str,required=True,help='input file to parse')
+ etfs_parser.add_argument('--no_output',action="store_true",help='skip output')
+ etfs_parser.set_defaults(func=etfs)
+
+ # tex_to_yaml
+ tty_parser = subparsers.add_parser("tex_to_yaml")
+ tty_parser.add_argument("--file", type=str,required=True,help='file contains name of data file')
+ tty_parser.add_argument("--format", type=str, required=False,help='''format contains string of data format (not necessary for covariance)
+ A guide: i -- independent variable,
+ d -- dependent variable,
+ stat -- statistical error,
+ sys -- systematic error''')
+ tty_parser.add_argument("--covariance", action="store_true", default=False,help='Flag to say whether the data is a covariance matrix or not') #
+ tty_parser.add_argument("--correlation", action="store_true", default=False,help='Same as covariance, but for a correlation matrix') #
+ tty_parser.add_argument("--qualifiers", type=str, default="None",help='qualifiers contains name of qualifiers file, defaults to "None"')
+ tty_parser.add_argument("--remove", nargs='+', help="list of terms to remove from table")
+ tty_parser.set_defaults(func=tty)
+
+ # make_submission_yaml_file
+ msyf_parser = subparsers.add_parser("prepare_submission",
+ description="Preparation of submission.yaml file for HepData submission. "
+ "Requires the data yaml files produced from tex_to_yaml to be provided")
+ msyf_parser.add_argument('-f','--files',type=str,nargs='+',required=True,help='input yaml file(s) to parse. Note, can pass *.yaml')
+ msyf_parser.set_defaults(func=msyf)
+
+ args = parser.parse_args()
+ args.func(args)
diff --git a/extract_tables_from_source.py b/src/HepDataExtractor/extract_tables_from_source.py
similarity index 59%
rename from extract_tables_from_source.py
rename to src/HepDataExtractor/extract_tables_from_source.py
index da6e2c0ecdf5dff7cf853cfc7419ec7d669dec9c..e91393a83e5e0d2f6a6c32c829ee34243784ab46 100644
--- a/extract_tables_from_source.py
+++ b/src/HepDataExtractor/extract_tables_from_source.py
@@ -1,3 +1,13 @@
+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration #
+# #
+# This software is distributed under the terms of the GNU General Public #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING". #
+# #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization #
+# or submit itself to any jurisdiction. #
+###############################################################################
import sys,os
def extract_tables(sourcefile):
@@ -14,42 +24,36 @@ def extract_tables(sourcefile):
return tables_in_paper
with open(sourcefile) as f:
- lines = f.readlines()
+ lines = f.readlines()
for i in range(len(lines)):
if 'begin{table}' in lines[i] or 'begin{sidewaystable}' in lines[i]:
# print('starting table')
temptable = []
j=0
- while not "\end" in lines[i+j]:
- if "\label" in lines[i+j]:
- temptablename = lines[i+j].split("\label{")[1].split("}")[0].replace("tab:","")
+ while not r"\end" in lines[i+j]:
+ if r"\label" in lines[i+j]:
+ temptablename = lines[i+j].split(r"\label{")[1].split("}")[0].replace("tab:","")
if not 'begin{' in lines[i+j]:
temptable.append(lines[i+j])
j+=1
-
+
tables_in_paper[temptablename]=temptable
- if '\input' in lines[i]:
+ if r'\input' in lines[i]:
#skip commented inputs
- if "%" in lines[i]: continue
- extended_file = lines[i].split("\input{")[1].split("}")[0]+".tex"
+ if "%" in lines[i]: continue
+ extended_file = lines[i].split(r"\input{")[1].split("}")[0]+".tex"
#pathological case where people also include .tex in input command
if ".tex.tex" in extended_file:
extended_file = extended_file.replace(".tex.tex",".tex")
path_to_included_file = os.path.join(full_path_to_sourcefile,extended_file)
-
+
extended_dict = extract_tables(path_to_included_file)
-
+
tables_in_paper = tables_in_paper | extended_dict
return tables_in_paper
-if '__main__'==__name__:
- import argparse
- parser = argparse.ArgumentParser()
- parser.add_argument('-f','--file',type=str,required=True,help='input file to parse')
- parser.add_argument('--no_output',action="store_true",help='skip output')
-
- args = parser.parse_args()
+def main(args):
print('now parsing',args.file)
tables_in_paper = extract_tables(args.file)
@@ -62,4 +66,4 @@ if '__main__'==__name__:
f.close()
else:
print('here is the output of the tables')
- print(tables_in_paper)
\ No newline at end of file
+ print(tables_in_paper)
diff --git a/make_submission_yaml_file.py b/src/HepDataExtractor/make_submission_yaml_file.py
similarity index 80%
rename from make_submission_yaml_file.py
rename to src/HepDataExtractor/make_submission_yaml_file.py
index 2a89e229069880732c95ffc9a6ec914ff616837d..84e2cc3c0a462074956ed50deab7013a9259a63f 100644
--- a/make_submission_yaml_file.py
+++ b/src/HepDataExtractor/make_submission_yaml_file.py
@@ -1,3 +1,13 @@
+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration #
+# #
+# This software is distributed under the terms of the GNU General Public #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING". #
+# #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization #
+# or submit itself to any jurisdiction. #
+###############################################################################
import sys,os
import argparse
@@ -12,7 +22,7 @@ import yaml
def get_metadata_info_for_yaml(input_yaml):
"""
Simple wrapper to get the metadata information necessary for the submission.yaml file.
- Uses safe_substitute on the template in the Templates directory to ensure return even
+ Uses safe_substitute on the template in the Templates directory to ensure return even
in the case of error.
"""
conf = yaml.safe_load(open(input_yaml,'r'))
@@ -33,7 +43,7 @@ def get_metadata_info_for_yaml(input_yaml):
if 'Covariance' in thing['header']['name'] or 'Correlation' in thing['header']['name']:
# print('skipping observables addition for correlation/covariance')
the_dict['special']=str(thing['header']['name'])
- else:
+ else:
observables.append(thing['header']['name'])
for thing in conf['independent_variables']:
# print('now appending independent variables',thing['header']['name'])
@@ -45,18 +55,13 @@ def get_metadata_info_for_yaml(input_yaml):
else:
vars_sorted = list(OrderedDict.fromkeys(independent_vars))
# the_dict['description'] = the_dict['special'] + ' for ' +', '.join(vars_sorted)
-
+
the_template = Template(open(os.path.dirname(os.path.abspath(__file__))+"/Templates/submission_template.yaml",'r').read())
return the_template.safe_substitute(the_dict)
-if '__main__'==__name__:
- parser = argparse.ArgumentParser(description="Preparation of submission.yaml script for hepdata submission.\
- Requires the data yaml files produced from tex_to_yaml.py to be provided")
- parser.add_argument('-f','--files',type=str,nargs='+',required=True,help='input yaml file(s) to parse. Note, can pass *.yaml')
- args = parser.parse_args()
-
+def main(args):
for f in args.files:
if not '.yaml' in f:
print("You haven't passed valid yaml files! Please try again")
@@ -89,7 +94,7 @@ if '__main__'==__name__:
submission_file.write('\n')
submission_file.write("---\n")
submission_file.write('\n')
-
-
+
+
submission_file.close()
- print('Done!')
\ No newline at end of file
+ print('Done!')
diff --git a/tex_to_yaml.py b/src/HepDataExtractor/tex_to_yaml.py
similarity index 87%
rename from tex_to_yaml.py
rename to src/HepDataExtractor/tex_to_yaml.py
index a61cb63de5e5d01d858ac28cd00d1d6e7c582a83..8a646f8c139a3173d335e08c1db9f6624b96a0d8 100644
--- a/tex_to_yaml.py
+++ b/src/HepDataExtractor/tex_to_yaml.py
@@ -1,3 +1,13 @@
+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration #
+# #
+# This software is distributed under the terms of the GNU General Public #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING". #
+# #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization #
+# or submit itself to any jurisdiction. #
+###############################################################################
import argparse
import numpy as np
import re
@@ -59,7 +69,7 @@ class value:
else:
output = " - value: " + str(self.x) + "\n"
return output
-
+
class variable:
"""
Variable class to contain the column header and each value the variable takes, with uncertainties
@@ -90,7 +100,7 @@ def discard(line):
line = line.strip(" \n\t~{}")
if line == "":
return True
- elif line.startswith("\multicolumn"):
+ elif line.startswith(r"\multicolumn"):
return False
elif line[0] == "%" or line[0] == "\\":
return True
@@ -101,7 +111,7 @@ def extract_header(string):
"""
Extracts the name and units (if any) from the header of a column and returns a string suitable for yaml
"""
- string = string.replace("\\xspace", "").replace("\\kern", "").replace("\\,", "").replace("\\!", "").replace("-0.1em", "").strip(" \n\t~\\")
+ string = string.replace(r"\xspace", "").replace(r"\kern", "").replace(r"\,", "").replace(r"\!", "").replace("-0.1em", "").strip(" \n\t~\\")
if string.startswith("multicolumn"): #Removes leading multicolumn expression from header
string = string[string.find("}")+1:]
string = string[string.find("}")+1:]
@@ -122,16 +132,16 @@ def extract_description(string):
Extract the description field from the caption listed in paper
"""
temp_string = string.replace("\\n","").replace("\\xspace","").replace("\\","").rstrip().strip()
-
+
if 'label' in temp_string:
- to_rep = re.findall("label\{[tab:]*[a-zA-Z_]*\}",temp_string)
+ to_rep = re.findall(r"label{[tab:]*[a-zA-Z_]*}",temp_string)
for rep in to_rep:
temp_string = temp_string.replace(rep,"")
temp_string = temp_string.replace('caption{',"").replace("}","")
return temp_string
-def split_format(string):
+def split_format(string):
"""
Splits format string so that each variable is its own string in a list
"""
@@ -143,7 +153,7 @@ def split_format(string):
temp_list[-1].append(i)
return temp_list
-def format_value(string):
+def format_value(string):
"""
Takes string with errors separated by commas and returns value object
"""
@@ -161,7 +171,7 @@ def format_value(string):
return the_val
-def write_variables(variable_list, file):
+def write_variables(variable_list, file):
"""
Writes variable objects in list to a yaml file
"""
@@ -173,7 +183,7 @@ def write_variables(variable_list, file):
for i in variable_list:
if i.is_indep == False:
file.write(repr(i))
-
+
def write_description(description,file):
"""
@@ -185,11 +195,11 @@ def remove_phantoms(string): #
"""
Removes \\phantom{...} from string
"""
- while "\phantom" in string:
- x = string.find("\phantom")
+ while r"\phantom" in string:
+ x = string.find(r"\phantom")
while string[x] != "}":
x += 1
- string = string[:string.find("\phantom")] + string[x+1:]
+ string = string[:string.find(r"\phantom")] + string[x+1:]
return string
def asym_unc(string):
@@ -201,20 +211,7 @@ def asym_unc(string):
-if '__main__'==__name__:
- parser = argparse.ArgumentParser()
- parser.add_argument("--file", type=str,required=True,help='file contains name of data file')
- parser.add_argument("--format", type=str, required=False,help='format contains string of data format (not necessary for covariance)\n\
- A guide: i -- independent variable,\
- d -- dependent variable, \
- stat -- statistical error,\
- sys -- systematic error')
- parser.add_argument("--covariance", action="store_true", default=False,help='Flag to say whether the data is a covariance matrix or not') #
- parser.add_argument("--correlation", action="store_true", default=False,help='Same as covariance, but for a correlation matrix') #
- parser.add_argument("--qualifiers", type=str, default="None",help='qualifiers contains name of qualifiers file, defaults to "None"')
- parser.add_argument("--remove", nargs='+', help="list of terms to remove from table")
-
- args = parser.parse_args()
+def main(args):
description = None
if args.covariance==False and args.correlation == False and args.format ==None:
print('Must pass format if not passing a correlation or covariance matrix!')
@@ -234,20 +231,20 @@ if '__main__'==__name__:
for i in lines:
if discard(i) == False: #Only valid lines
if args.covariance == True or args.correlation == True:
- data_array.append(remove_phantoms(i).replace("\\hline", "").strip(" \n\t~\\").split("&")) #Splits into array by &
+ data_array.append(remove_phantoms(i).replace(r"\hline", "").strip(" \n\t~\\").split("&")) #Splits into array by &
else:
if len(data_array) == 0: #Does not take convert the first line to values, as this contains headers
- data_array.append(remove_phantoms(i).replace("\\hline", "").strip(" \n\t~\\").split("&"))
+ data_array.append(remove_phantoms(i).replace(r"\hline", "").strip(" \n\t~\\").split("&"))
else:
- line_split = remove_phantoms(i).replace("\\hline", "").strip(" \n\t~\\$").split("&")
- if "\pm" in line_split: #Removes items that are just \pm
- line_split.remove("\pm")
- if " \pm " in line_split:
- line_split.remove(" \pm ")
+ line_split = remove_phantoms(i).replace(r"\hline", "").strip(" \n\t~\\$").split("&")
+ if r"\pm" in line_split: #Removes items that are just \pm
+ line_split.remove(r"\pm")
+ if r" \pm " in line_split:
+ line_split.remove(r" \pm ")
count = 0 #Count iterates in the format string to determine whether each number is a indep value, dep value, sys uncertainty, etc.
value_list = [] #List of values extracted from this line
for j in line_split: #For item in line split by "&"
- temp = j.split("\pm")
+ temp = j.split(r"\pm")
temp = [x.strip(" \n\t~\\$") for x in temp]
if len(temp) > 1: #Removes blank characters from temp
if "" in temp:
@@ -296,7 +293,7 @@ if '__main__'==__name__:
else:
variables.append(variable(True, indep_header, "None"))
variables.append(variable(True, indep_header, "None"))
- if args.covariance == True:
+ if args.covariance == True:
variables.append(variable(False, "name: Covariance", args.qualifiers))
else:
variables.append(variable(False, "name: Correlation", args.qualifiers))
@@ -341,14 +338,14 @@ if '__main__'==__name__:
for i in range(1,len(data_array)):
for j in range(len(data_array[i,:])):
variables[j].append(data_array[i,j])
-
+
output_file = open(args.file.replace(".tex", ".yaml"), "w") #Creates file with same name, but .yaml instead of .tex
-
+
write_variables(variables, output_file) #Writes contents of variables list to file
- output_file.close()
+ output_file.close()
#write extra file for description
-
+
if description is not None:
output_description_file = open(args.file.replace('.tex','_description_file.txt'),'w')
write_description(description, output_description_file)
- output_description_file.close()
\ No newline at end of file
+ output_description_file.close()