Merge pull request #77 from smithlabcode/adding-tests

Adding tests

Makefile.am

@@ -14,15 +14,36 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 # General Public License for more details.
 
-EXTRA_DIST = README.md LICENSE preseqR data docs
 ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp
 install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
 AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp
+AM_CPPFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
 
 CXXFLAGS = -O2 # default has optimization on
 
+EXTRA_DIST = \
+	README.md \
+	LICENSE \
+	preseqR \
+	data \
+	docs \
+	tests/md5sum.txt \
+	tests/data/lc_extrap_input.vals \
+	tests/data/gc_extrap_input.mr \
+	tests/data/c_curve_input.hist \
+	tests/scripts/test_c_curve.test \
+	tests/scripts/test_gc_extrap.test \
+	tests/scripts/test_lc_extrap.test
+
+TESTS = \
+	tests/scripts/test_c_curve.test \
+	tests/scripts/test_lc_extrap.test \
+	tests/scripts/test_gc_extrap.test
+
+TEST_EXTENSIONS = .test
+
 LDADD = src/smithlab_cpp/libsmithlab_cpp.a
 
 bin_PROGRAMS = preseq

configure.ac

@@ -47,4 +47,13 @@ AS_IF([test "x$enable_hts" = "xyes"],
 AM_CONDITIONAL([ENABLE_HTS], [test "x$enable_hts" = "xyes"])
 
 AC_CONFIG_FILES([Makefile])
+
+dnl make the test data files available in the build tree
+AC_CONFIG_LINKS([
+tests/md5sum.txt:tests/md5sum.txt
+tests/c_curve_input.hist:tests/data/c_curve_input.hist
+tests/lc_extrap_input.vals:tests/data/lc_extrap_input.vals
+tests/gc_extrap_input.mr:tests/data/gc_extrap_input.mr
+])
+
 AC_OUTPUT

documentation/docs/requirements.txt

@@ -1,8 +1,8 @@
-jinja2==3.0.3
+jinja2>=3.1.4
 mkdocs>=1.3.1
 babel>=2.9.0
 click>=7.0
-Jinja2>=2.10.2
+Jinja2>=3.1.4
 Markdown>=3.2.1,<3.4
 PyYAML>=5.2
 watchdog>=2.0.0

tests/data/c_curve_input.hist

@@ -0,0 +1,18 @@
+1	982419
+2	6060
+3	214
+4	63
+5	32
+6	21
+7	14
+8	9
+9	6
+10	3
+11	6
+12	2
+13	2
+14	2
+15	3
+16	2
+24	2
+31	1