Merge pull request #271 from rmcolq/0.9.0-rc1-branch

0.9.0 -> 0.9.0-rc1

.gitignore

@@ -65,20 +65,6 @@ EcoliK12_pandora*
 # local directory - michael
 vm-build/
 
-# local directory - leandro
-Singularity_debug.pandora
-debug_with_singularity.sh
-pandora_debug.img
-build_debug*
-build/
-data_issue*
-build_release*
-build_profiling*
-docker/
-
-mounted_folder/
-
-docker_dev/
 CMakeCache.txt
 CMakeFiles
 CTestTestfile.cmake
@@ -100,33 +86,16 @@ cmake_install.cmake
 compile_commands.json
 pandora
 
-example/output_toy_example_no_denovo/
-example/prgs/kmer_prgs/
-example/prgs/toy_prg.fa.k15.w14.idx
-example/pandora-latest.simg
-example/pandora_workflow
-!example/msas/GC00006032.fa
-!example/msas/GC00010897.fa
-!example/pandorupdated_prgsa_workflow_data/assemblies/samples/toy_sample_1/toy_sample_1.ref.fa
-!example/pandora_workflow_data/assemblies/samples/toy_sample_2/toy_sample_2.ref.fa
-!example/prgs/toy_prg.fa
-!example/scripts/data/ref_to_get_reads_from.toy_example_1.fa
-!example/scripts/data/ref_to_get_reads_from.toy_example_2.fa
 
-#portable binary build dir
-build_portable_executable
-pandora-linux-precompiled
-
-/cmake-build-release/
-example/pandora_discover
-example/venv
-/example/msas_output/
-/example/make_prg_0.2.0_prototype
-/example/pandora-linux-precompiled-v0.9.0
+!example/msas
+!example/reads
 /example/pandora_discover_out/
 /example/prgs/
-/example/output_toy_example_with_denovo/
+/example/output_toy_example*
 /example/updated_prgs/
-/example/pandora-linux-precompiled-v0.9.0.gz
+/example/pandora-linux-precompiled*
+/example/make_prg_*
 
-example/pandora-linux-precompiled-pandora_paper_tag1
+#portable binary build dir
+build_portable_executable
+pandora-linux-precompiled

CHANGELOG.md

@@ -9,7 +9,7 @@ project adheres to
 
 ## [Unreleased]
 
-## [0.9.0]
+## [0.9.0-rc1]
 
 ### Changed
 - `pandora discover` now receives read index files describing samples and reads, and discover denovo sequences in these samples.
@@ -85,7 +85,8 @@ from this point will have their changes meticulously documented here.
 
 - k-mer coverage underflow bug in `LocalPRG` [[#183][183]]
 
-[Unreleased]: https://github.com/olivierlacan/keep-a-changelog/compare/0.8.0...HEAD
+[Unreleased]: https://github.com/rmcolq/pandora/compare/0.9.0-rc1...HEAD
+[0.9.0-rc1]: https://github.com/rmcolq/pandora/releases/tag/0.9.0-rc1
 [0.8.0]: https://github.com/rmcolq/pandora/releases/tag/0.8.0
 [v0.7.0]: https://github.com/rmcolq/pandora/releases/tag/v0.7.0
 

CMakeLists.txt

@@ -12,6 +12,7 @@ HunterGate(
 # project configuration
 set(PROJECT_NAME_STR pandora)
 project(${PROJECT_NAME_STR} VERSION "0.9.0" LANGUAGES C CXX)
+set(ADDITIONAL_VERSION_LABELS "-rc1")
 configure_file( include/version.h.in ${CMAKE_BINARY_DIR}/include/version.h )
 
 # add or not feature to print the stack trace

README.md

@@ -78,13 +78,13 @@ In this binary, all libraries are linked statically.
 
 * **Download**:
   ```
-  wget https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0
+  wget https://github.com/rmcolq/pandora/releases/download/0.9.0-rc1/pandora-linux-precompiled-v0.9.0-rc1
   ```
 
 * **Running**:
 ```
-chmod +x pandora-linux-precompiled-v0.9.0
-./pandora-linux-precompiled-v0.9.0 -h
+chmod +x pandora-linux-precompiled-v0.9.0-rc1
+./pandora-linux-precompiled-v0.9.0-rc1 -h
 ```
 
 * **Notes**:

example/run_pandora.sh

@@ -2,8 +2,8 @@
 set -eu
 
 # configs
-pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0"
-pandora_executable="./pandora-linux-precompiled-v0.9.0"
+pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.0-rc1/pandora-linux-precompiled-v0.9.0-rc1"
+pandora_executable="./pandora-linux-precompiled-v0.9.0-rc1"
 make_prg_URL="https://github.com/leoisl/make_prg/releases/download/v0.2.0_prototype/make_prg_0.2.0_prototype"
 make_prg_executable="./make_prg_0.2.0_prototype"
 

include/version.h.in

@@ -1,6 +1,6 @@
 #ifndef VERSION_H
 #define VERSION_H
 
-#define PANDORA_VERSION "@PROJECT_VERSION@"
+#define PANDORA_VERSION "@PROJECT_VERSION@""@ADDITIONAL_VERSION_LABELS@"
 
 #endif // VERSION_H