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Develop #54

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merged 32 commits into from
Feb 17, 2024
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b4d1c4c
- renamed exists to contains
mhekkel Jan 17, 2024
e09913a
- checking and optionally dropping ndb_poly_seq_scheme
mhekkel Jan 22, 2024
7e4d2ff
formatting data in reconstruction
mhekkel Jan 22, 2024
afc541b
Merge remote-tracking branch 'github/develop-cif2fasta' into develop
mhekkel Jan 22, 2024
369a83b
Version bump
mhekkel Jan 22, 2024
bbd1e27
Attempt to get code compiling on macOS
mhekkel Jan 22, 2024
fc14a65
attempt 2 to build on macOS
mhekkel Jan 22, 2024
f450643
Added remove column
mhekkel Jan 22, 2024
5d4534f
Added rename_column
mhekkel Jan 22, 2024
13ab1ca
macOS...
mhekkel Jan 22, 2024
fb2b1e9
Fixed serious bug in emplace of both datablock and file.
mhekkel Jan 22, 2024
2792cae
renaming field and column to item
mhekkel Jan 23, 2024
a5d4399
replace tag with item or item_name
mhekkel Jan 23, 2024
30a2ebd
Merge remote-tracking branch 'github/develop-cif2fasta' into develop
mhekkel Jan 23, 2024
5320cb1
Fix validate pdbx
mhekkel Jan 23, 2024
db603e5
version bump
mhekkel Jan 23, 2024
4e19d54
atom_site_anisotrop check
mhekkel Jan 23, 2024
e597503
- changed compound::is_known_peptide/is_know_base
mhekkel Jan 24, 2024
12ee4a7
pdb2cif work
mhekkel Jan 29, 2024
4e012cb
gcc diagnostics and clipper
mhekkel Jan 29, 2024
446438b
Fixing pdb2cif, and sequence checking
mhekkel Jan 29, 2024
ab781d4
work around bug in old gcc
mhekkel Jan 29, 2024
3f93c27
fix reconstruct sequence
mhekkel Jan 29, 2024
75a5f79
formatting
mhekkel Jan 30, 2024
0e83bc3
some small optimisations
mhekkel Jan 30, 2024
04147a2
Fix url in compound message
mhekkel Jan 30, 2024
f02e59d
Fix operator= for item_handle
mhekkel Jan 30, 2024
2fed7a7
Fix operator= for item_handle
mhekkel Jan 30, 2024
9a3eced
new update_value in category
mhekkel Jan 31, 2024
d94f6f4
test builds faster now
mhekkel Feb 5, 2024
9c78131
Use Catch2 version 3 if installed
mhekkel Feb 17, 2024
be738e7
catch22
mhekkel Feb 17, 2024
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,5 @@ Testing/
include/cif++/exports.hpp
docs/api
docs/conf.py
build_ci/
build_ci/
data/components.cif
52 changes: 2 additions & 50 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ cmake_minimum_required(VERSION 3.16)
# set the project name
project(
libcifpp
VERSION 6.1.0
VERSION 7.0.0
LANGUAGES CXX)

list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
Expand Down Expand Up @@ -546,55 +546,7 @@ if(NOT PROJECT_IS_TOP_LEVEL)
endif()

if(BUILD_TESTING)
# We're using the older version 2 of Catch2
FetchContent_Declare(
Catch2
GIT_REPOSITORY https://github.com/catchorg/Catch2.git
GIT_TAG v2.13.9)

FetchContent_MakeAvailable(Catch2)

list(
APPEND
CIFPP_tests
unit-v2
unit-3d
format
model
rename-compound
sugar
spinner
validate-pdbx)

foreach(CIFPP_TEST IN LISTS CIFPP_tests)
set(CIFPP_TEST "${CIFPP_TEST}-test")
set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")

add_executable(
${CIFPP_TEST} ${CIFPP_TEST_SOURCE}
"${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")

target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
Catch2::Catch2)
target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")

if(MSVC)
# Specify unwind semantics so that MSVC knowns how to handle exceptions
target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
endif()

add_custom_target(
"run-${CIFPP_TEST}"
DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})

add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
${CMAKE_CURRENT_SOURCE_DIR}/test)

add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
${CMAKE_CURRENT_SOURCE_DIR}/test)
endforeach()
add_subdirectory(test)
endif()

# Optionally install the update scripts for CCD and dictionary files
Expand Down
9 changes: 9 additions & 0 deletions changelog
Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
Version 7.0.0
- Renaming many methods and parameters to be more
consistent with the mmCIF dictionaries.
(Most notably, item used to be called column or
tag sometimes).
- validation_error is now a std::system_error error
value. The exception is gone.
- Added repairSequenceInfo to repair invalid files

Version 6.1.0
- Add formula weight to entity in pdb2cif
- Change order of categories inside a datablock to match order in file
Expand Down
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