clean up repo root: move capnp schema, mkdocs config into subdirs

Author: amkram

.dockerignore

@@ -1,11 +1,9 @@
 .git
-.vscode
+.github
 .claude
+.vscode
 build
-external_cache
+output
+site
 docs
-examples
 recipe
-scripts
-*.md
-LICENSE

.github/workflows/docs.yml

@@ -3,7 +3,7 @@ name: Deploy docs
 on:
   push:
     branches: [main]
-    paths: [docs/**, mkdocs.yml]
+    paths: [docs/**]
 
 permissions:
   contents: read
@@ -22,7 +22,7 @@ jobs:
         with:
           python-version: '3.12'
       - run: pip install mkdocs-material
-      - run: mkdocs build
+      - run: mkdocs build -f docs/mkdocs.yml
       - uses: actions/upload-pages-artifact@v3
         with:
           path: site

CMakeLists.txt

@@ -139,7 +139,7 @@ message(STATUS "Building CapnProto from bundled source")
 include_directories(${CAPNP_INSTALL_DIR}/include)
 
 # Add index_lite.capnp generation (the only capnp schema used)
-set(LITE_CAPNP_SRC_FILE "${CMAKE_CURRENT_SOURCE_DIR}/index_lite.capnp")
+set(LITE_CAPNP_SRC_FILE "${CMAKE_CURRENT_SOURCE_DIR}/src/index_lite.capnp")
 set(LITE_CAPNP_GEN_DIR "${CMAKE_CURRENT_BINARY_DIR}")
 set(LITE_CAPNP_GEN_CPP "${LITE_CAPNP_GEN_DIR}/index_lite.capnp.c++")
 set(LITE_CAPNP_GEN_H "${LITE_CAPNP_GEN_DIR}/index_lite.capnp.h")

Dockerfile

@@ -15,24 +15,18 @@ RUN apt-get update && apt-get install -y \
   libboost-system-dev \
   libboost-date-time-dev \
   zlib1g-dev \
+  libhts-dev \
   capnproto \
   libcapnp-dev \
-  autoconf \
-  automake \
-  libtool \
   libeigen3-dev \
   && rm -rf /var/lib/apt/lists/*
 
-
 WORKDIR /home/panmap
 
 COPY . .
 
-RUN mkdir -p build && \
-  cd build && \
-  cmake .. && make MAKEFLAGS= -j$(nproc)
+RUN mkdir -p build && cd build && cmake .. && make -j$(nproc)
 
 ENV PATH="/home/panmap/build/bin:${PATH}"
 
 CMD ["panmap"]
-

mkdocs.yml docs/mkdocs.ymlmkdocs.yml renamed to docs/mkdocs.yml

@@ -2,6 +2,8 @@ site_name: panmap
 site_description: Pangenome-based sequence placement, alignment, and genotyping
 repo_url: https://github.com/amkram/panmap
 repo_name: amkram/panmap
+docs_dir: .
+site_dir: ../site
 
 theme:
   name: material

recipe/CMakeLists.txt

@@ -37,7 +37,7 @@ include_directories(SYSTEM ${Protobuf_INCLUDE_DIRS})
 # ===== CapnProto code generation =====
 add_custom_target(capnp_tools ALL)
 
-set(LITE_CAPNP_SRC_FILE "${CMAKE_CURRENT_SOURCE_DIR}/index_lite.capnp")
+set(LITE_CAPNP_SRC_FILE "${CMAKE_CURRENT_SOURCE_DIR}/src/index_lite.capnp")
 set(LITE_CAPNP_GEN_DIR "${CMAKE_CURRENT_BINARY_DIR}")
 set(LITE_CAPNP_GEN_CPP "${LITE_CAPNP_GEN_DIR}/index_lite.capnp.c++")
 set(LITE_CAPNP_GEN_H "${LITE_CAPNP_GEN_DIR}/index_lite.capnp.h")