Merge pull request #314 from rmcolq/0.10.0-alpha.0_branch

Prepare 0.10.0-alpha.0 release

.dockerignore

@@ -21,6 +21,5 @@ cmake_install.cmake
 compile_commands.json
 Makefile
 pandora.cbp
-build_portable_executable
-pandora-linux-precompiled
-/cmake-build-release/
+pandora-linux-precompiled*
+example

.github/workflows/ci.yaml

@@ -0,0 +1,42 @@
+name: Pandora CI
+
+on: [ push, pull_request ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Install dependencies
+        run: |
+          sudo apt update && sudo apt install cmake
+      - name: Check out code for the build
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      # TODO: add format step back (last PR before release)
+#      - name: "Format"
+#        run: |
+#          find src/ include/ test/ -type f \( -iname \*.h -o -iname \*.cpp \) | xargs -I _ clang-format -style=file -output-replacements-xml _ | grep -c "<replacement " >/dev/null
+#          if [ $? -ne 1 ]; then echo "Not all source and header files are formatted with clang-format"; exit 1; fi
+
+      - name: Build and test release build
+        run: |
+          mkdir build_release && cd build_release
+          cmake -DCMAKE_BUILD_TYPE=Release -DHUNTER_JOBS_NUMBER=4 ..
+          make -j4
+          ctest -V
+          ./pandora --help
+          cd ..
+
+      - name: Build and test debug build
+        run: |
+          mkdir build_debug && cd build_debug
+          cmake -DCMAKE_BUILD_TYPE=Debug -DHUNTER_JOBS_NUMBER=4 ..
+          make -j4
+          ctest -V
+          ./pandora --help
+          cd ..

.gitignore

@@ -103,6 +103,6 @@ pandora-linux-precompiled*
 /archives/
 /example/out/
 
-example/make_prg.sif
+example/make_prg*
 /scripts/measure_performance_from_log/.ipynb_checkpoints/
 /build_test/

CHANGELOG.md

@@ -7,6 +7,21 @@ this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+## [0.10.0-alpha.0]
+
+### Changed
+
+- Denovo discovery is now done by repeatedly polishing the loci's maximum likelihood sequences using the regions of the
+reads that mapped to the loci through [Racon](Racon);
+- Pandora `discover` CLI heavily changed: parameters `-M,--mapped-reads`, `--clean-dbg`, `--discover-k`, `--max-ins`,
+`--covg-threshold`, `-l`, `-L`, `-d,--merge`, `-N`, `--min-dbg-dp` removed;
+
+### Added
+- Pandora `map`, `compare` and `discover` commands now produce [SAM](SAM) files;
+- Parameter `-K`/`--debugging-files` to pandora `map`, `compare` and `discover` commands to create extra
+debugging files, which are able to describe completely the mapping process of `pandora`.
+
+
 ## [0.9.2]
 
 ### Changed
@@ -123,7 +138,7 @@ their changes meticulously documented here.
 
 - k-mer coverage underflow bug in `LocalPRG` [[#183][183]]
 
-[Unreleased]: https://github.com/rmcolq/pandora/compare/0.9.1...HEAD
+[Unreleased]: https://github.com/rmcolq/pandora/compare/0.10.0-alpha.0...HEAD
 [0.9.2]: https://github.com/rmcolq/pandora/compare/0.9.2...0.9.1
 [0.9.1]: https://github.com/rmcolq/pandora/releases/tag/0.9.1
 [0.9.0]: https://github.com/rmcolq/pandora/releases/tag/0.9.0
@@ -140,4 +155,5 @@ their changes meticulously documented here.
 [265]: https://github.com/rmcolq/pandora/pull/265
 [294]: https://github.com/rmcolq/pandora/issues/294
 [v0.7.0]: https://github.com/rmcolq/pandora/releases/tag/v0.7.0
-
+[Racon]: https://github.com/lbcb-sci/racon
+[SAM]: https://samtools.github.io/hts-specs/SAMv1.pdf

CMakeLists.txt

@@ -12,7 +12,7 @@ HunterGate(
 
 # project configuration
 set(PROJECT_NAME_STR pandora)
-project(${PROJECT_NAME_STR} VERSION "0.9.2" LANGUAGES C CXX)
+project(${PROJECT_NAME_STR} VERSION "0.10.0" LANGUAGES C CXX)
 set(ADDITIONAL_VERSION_LABELS "")
 configure_file( include/version.h.in ${CMAKE_BINARY_DIR}/include/version.h )
 

Dockerfile

@@ -1,7 +1,7 @@
 # PANDORA
 # Pan-genome inference and genotyping with long noisy or short accurate reads
 
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 ENV LC_ALL C.UTF-8
 ENV LANG C.UTF-8
@@ -11,7 +11,6 @@ RUN apt update \
     && apt-add-repository universe \
     && apt update \
     && apt install --no-install-recommends -y build-essential git cmake wget gdb \
-                   minimap2=2.17+dfsg-2 mafft=7.453-1 racon=1.4.10-1build1 \
     && rm -rf /var/lib/apt/lists/* \
     && apt-get clean
 
@@ -27,7 +26,7 @@ COPY . $PANDORA_DIR
 WORKDIR ${PANDORA_DIR}/build
 RUN cmake -DCMAKE_BUILD_TYPE="$PANDORA_BUILD_TYPE" -DHUNTER_JOBS_NUMBER=4 .. \
     && make -j4 \
-    # && ctest -V \  # TODO: add tests back
+    && ctest -V \
     && apt-get remove -y cmake git \
     && mv pandora /bin/pandora \
     && cd / \

README.md

@@ -1,7 +1,7 @@
-| Branch             | Status                                                                           |
-|:-------------------|:---------------------------------------------------------------------------------|
-| [`master`][master] | ![Travis (.com) branch](https://img.shields.io/travis/com/rmcolq/pandora/master) |
-| [`dev`][dev]       | ![Travis (.com) branch](https://img.shields.io/travis/com/rmcolq/pandora/dev)    |
+| Branch             | Status                                                                                                |
+|:-------------------|:------------------------------------------------------------------------------------------------------|
+| [`master`][master] | ![master branch badge](https://github.com/rmcolq/pandora/actions/workflows/ci.yaml/badge.svg)         |
+| [`dev`][dev]       | ![dev branch badge](https://github.com/rmcolq/pandora/actions/workflows/ci.yaml/badge.svg?branch=dev) |
 
 [master]: https://github.com/rmcolq/pandora/tree/master
 [dev]: https://github.com/rmcolq/pandora/tree/dev
@@ -31,7 +31,7 @@ Pandora is a tool for bacterial genome analysis using a pangenome reference grap
 The PanRG is a collection of 'floating'
 local graphs (PRGs), each representing some orthologous region of interest
 (e.g. genes, mobile elements or intergenic regions). See
-https://github.com/leoisl/make_prg for a tool which can construct
+[make_prg][make_prg] for a tool which can construct
 these PanRGs from a set of aligned sequence files.
 
 Pandora can do the following for a single sample (read dataset):
@@ -81,13 +81,13 @@ In this binary, all libraries are linked statically.
 
 * **Download**:
   ```
-  wget https://github.com/rmcolq/pandora/releases/download/0.9.2/pandora-linux-precompiled-v0.9.2
+  wget https://github.com/rmcolq/pandora/releases/download/0.10.0-alpha.0/pandora-linux-precompiled-v0.10.0-alpha.0
   ```
 
 * **Running**:
 ```
-chmod +x pandora-linux-precompiled-v0.9.2
-./pandora-linux-precompiled-v0.9.2 -h
+chmod +x pandora-linux-precompiled-v0.10.0-alpha.0
+./pandora-linux-precompiled-v0.10.0-alpha.0 -h
 ```
 
 * **Notes**:
@@ -150,3 +150,4 @@ See [Usage](https://github.com/rmcolq/pandora/wiki/Usage).
 
 <!--Link References-->
 [pandora_2020_paper]: https://doi.org/10.1186/s13059-021-02473-1
+[make_prg]: https://github.com/iqbal-lab-org/make_prg/

example/README.md

@@ -4,11 +4,8 @@ Here we present a walkthrough of running `pandora` on a toy example. We run:
 1) `pandora` without de novo discovery;
 2) `pandora` with de novo discovery (see Figure 2 of [our paper][pandora_2020_paper]).
 
-## Dependencies
 * **There is no need to have `pandora` or `make_prg` installed. The running script will automatically download
-  and run the precompiled binary for `pandora` and a container through `singularity` for `make_prg`**;
-* `wget`;
-* `singularity 3.0+`;
+  and run the precompiled binaries for `pandora` and `make_prg`**;
 
 ## Input data description