Update documentation

4 files changed, 71 insertions, 3 deletions

diff --git a/doc/reference/CrystFEL-docs.sgml b/doc/reference/CrystFEL-docs.sgml
index 2f42f5e7..ffff9e9f 100644
--- a/doc/reference/CrystFEL-docs.sgml
+++ b/doc/reference/CrystFEL-docs.sgml
@@ -48,6 +48,11 @@
   </chapter>
 
   <chapter>
+    <title>Integer Matrices</title>
+        <xi:include href="xml/integer_matrix.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+  <chapter>
     <title>Simulation</title>
         <xi:include href="xml/simulation.xml"><xi:fallback /></xi:include>
   </chapter>
diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt
index 3ccc1511..8da5798c 100644
--- a/doc/reference/CrystFEL-sections.txt
+++ b/doc/reference/CrystFEL-sections.txt
@@ -60,11 +60,16 @@ read_reflections
 read_reflections_from_file
 asymmetric_indices
 res_cutoff
+check_list_symmetry
+copy_reflist
+find_equiv_in_list
 </SECTION>
 
 <SECTION>
 <FILE>unitcell</FILE>
 UnitCell
+LatticeType
+UnitCellTransformation
 <SUBSECTION>
 cell_new
 cell_new_from_cell
@@ -77,7 +82,9 @@ cell_get_cartesian
 cell_get_parameters
 cell_get_pointgroup
 cell_get_reciprocal
-cell_get_spacegroup
+cell_get_centering
+cell_get_lattice_type
+cell_get_unique_axis
 <SUBSECTION>
 cell_set_cartesian
 cell_set_cartesian_a
@@ -86,14 +93,22 @@ cell_set_cartesian_c
 cell_set_parameters
 cell_set_pointgroup
 cell_set_reciprocal
-cell_set_spacegroup
+cell_set_centering
+cell_set_lattice_type
+cell_set_unique_axis
 <SUBSECTION>
+cell_transform
+cell_transform_inverse
 tfn_combine
 tfn_identity
+tfn_from_intmat
 tfn_inverse
 tfn_print
 tfn_vector
 tfn_free
+<SUBSECTION>
+
+cell_rep
 </SECTION>
 
 <SECTION>
@@ -110,6 +125,9 @@ uncenter_cell
 bravais_lattice
 right_handed
 str_lattice
+uncenter_cell
+forbidden_reflection
+load_cell_from_pdb
 </SECTION>
 
 <SECTION>
@@ -213,6 +231,7 @@ index_pattern
 run_dirax
 run_mosflm
 indexingprivate
+map_all_peaks
 </SECTION>
 
 <SECTION>
@@ -238,11 +257,35 @@ is_centrosymmetric
 </SECTION>
 
 <SECTION>
+<FILE>integer_matrix</FILE>
+IntegerMatrix
+<SUBSECTION>
+intmat_new
+intmat_copy
+intmat_free
+<SUBSECTION>
+intmat_get
+intmat_set
+<SUBSECTION>
+intmat_intmat_mult
+intmat_intvec_mult
+intmat_det
+intmat_inverse
+<SUBSECTION>
+intmat_equals
+intmat_is_identity
+intmat_is_inversion
+<SUBSECTION>
+intmat_print
+</SECTION>
+
+<SECTION>
 <FILE>detector</FILE>
 copy_geom
 fill_in_values
 free_detector_geometry
 get_detector_geometry
+write_detector_geometry
 find_panel
 find_panel_by_name
 find_panel_number
@@ -252,6 +295,9 @@ get_pixel_extents
 get_q
 get_q_for_panel
 get_tt
+smallest_q
+reverse_2d_mapping
+largest_q
 </SECTION>
 
 <SECTION>
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 74f33bb2..174240b6 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -71,6 +71,8 @@
  *
  * Rotate a %UnitCell using a %quaternion.
  *
+ * Deprecated: 0.4.3.  Use tfn_random_rotation() and cell_transform() instead.
+ *
  * Returns: a newly allocated rotated copy of @in.
  *
  */
@@ -1045,6 +1047,21 @@ void cell_fudge_gslcblas()
 }
 
 
+/**
+ * rotate_cell:
+ * @in: A %UnitCell to rotate
+ * @omega: Euler angle about +z
+ * @phi: Euler angle about +x
+ * @rot: Euler angle about new +z
+ *
+ * Rotate a %UnitCell using Euler angles
+ *
+ * Deprecated: Deprecated since 0.4.3.  Use tfn_random_rotation() and
+ * cell_transform() instead.
+ *
+ * Returns: a newly allocated rotated copy of @in.
+ *
+ */
 UnitCell *rotate_cell(UnitCell *in, double omega, double phi, double rot)
 {
 	UnitCell *out;
diff --git a/libcrystfel/src/integer_matrix.c b/libcrystfel/src/integer_matrix.c
index ad38a9fe..32784f20 100644
--- a/libcrystfel/src/integer_matrix.c
+++ b/libcrystfel/src/integer_matrix.c
@@ -47,7 +47,7 @@
  * @include: "integer_matrix.h"
  * @Image:
  *
- * Routines to handle integer matrix
+ * An integer matrix library
  */