docs; makefile->autotools

KellisLab · Jan 9, 2024 · 1c75b4b · 1c75b4b
1 parent 1332bfc
commit 1c75b4b
Show file tree

Hide file tree

Showing 102 changed files with 10,026 additions and 79 deletions.
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -17,7 +17,7 @@ build:
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+   configuration: docs/pydocs/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
@@ -29,4 +29,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
-   - requirements: docs/requirements.txt
+   - requirements: pydocs/requirements.txt
diff --git a/Makefile b/Makefile
diff --git a/Makefile.am b/Makefile.am
@@ -0,0 +1,22 @@
+# Makefile.am
+
+document:
+	Rscript -e "devtools::document(roclets = c('rd', 'collate', 'namespace'))"
+
+buildbin:
+	Rscript -e "devtools::build(binary = TRUE, args = c('--preclean'))"
+
+buildsrc:
+	Rscript -e "devtools::build(args=c('--no-buildvignettes'))"
+
+install:
+	Rscript -e "devtools::install_local(force=TRUE, upgrade=FALSE)"
+
+test:
+	Rscript -e "devtools::test()"
+
+site:
+	Rscript -e "pkgdown::build_site(preview=FALSE)"
+
+
+all-local: document buildsrc buildbin install test site
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -0,0 +1 @@
+destination: "docs/rdocs"
diff --git a/configure.ac b/configure.ac
@@ -0,0 +1,37 @@
+AC_INIT([benj], [0.0.7])
+AC_CHECK_PROG([R_FOUND], [R], [yes], [no])
+if test "x$R_FOUND" = xno; then
+  AC_MSG_ERROR([R is required but it's not installed.])
+fi
+AC_CHECK_PROG([WGET_FOUND], [wget], [yes], [no])
+if test "x$WGET_FOUND" = xno; then
+  AC_MSG_ERROR([wget is required but it's not installed.])
+fi
+AC_PROG_MAKE_SET
+
+# Automake initialization
+AM_INIT_AUTOMAKE([foreign])
+
+# Define the directory where files should be downloaded
+TENX_DIR="inst/extdata/10x"
+AC_SUBST(TENX_DIR)
+
+# Create the extdata directory if it does not exist
+AC_MSG_CHECKING([for inst/extdata directory])
+AS_MKDIR_P([${TENX_DIR}])
+AC_MSG_RESULT([created])
+
+# Download files using wget if they don't exist
+AC_MSG_CHECKING([for required files])
+REQUIRED_FILES="Dual_Index_Kit_TT_Set_A.csv Dual_Index_Kit_NN_Set_A.csv Dual_Index_Kit_NT_Set_A.csv Single_Index_Kit_T_Set_A.csv Single_Index_Kit_N_Set_A.csv"
+for file in $REQUIRED_FILES; do
+  if test ! -f "${TENX_DIR}/$file"; then
+    AC_MSG_RESULT([missing $file, downloading...])
+    wget -P ${TENX_DIR} --no-check-certificate "https://cdn.10xgenomics.com/raw/upload/v1655151897/support/in-line documents/$file"
+  else
+    AC_MSG_RESULT([found $file])
+  fi
+done
+
+AC_CONFIG_FILES([Makefile])
+AC_OUTPUT
diff --git a/docs/Makefile → docs/pydocs/Makefile b/docs/Makefile → docs/pydocs/Makefile
diff --git a/docs/conf.py → docs/pydocs/conf.py b/docs/conf.py → docs/pydocs/conf.py
diff --git a/docs/deg.ipynb → docs/pydocs/deg.ipynb b/docs/deg.ipynb → docs/pydocs/deg.ipynb
diff --git a/docs/deg.rst → docs/pydocs/deg.rst b/docs/deg.rst → docs/pydocs/deg.rst
diff --git a/docs/index.rst → docs/pydocs/index.rst b/docs/index.rst → docs/pydocs/index.rst
diff --git a/docs/make.bat → docs/pydocs/make.bat b/docs/make.bat → docs/pydocs/make.bat
diff --git a/docs/requirements.txt → docs/pydocs/requirements.txt b/docs/requirements.txt → docs/pydocs/requirements.txt
diff --git a/docs/rdocs/404.html b/docs/rdocs/404.html