Resolve FIXMEs and TODOs

Prompted by the article linked below, for each FIXME/TODO I've either
referenced an issue in the tracker, or removed it if it's not worth
fixing.

https://schleiss.io/plotting-source-code-todos-for-open-source-projects

11 files changed, 10 insertions, 43 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 31ba9d35..30744bd4 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1332,8 +1332,7 @@ double lowest_reflection(UnitCell *cell)
 	signed int h, k, l;
 	double lowres = INFINITY;
 
-	/* FIXME: Inelegant and nasty.  Anyone want to work out
-	 * all the possible cases? */
+	/* Boring brute-force approach */
 	for ( h=0; h<4; h++ ) {
 		for ( k=0; k<4; k++ ) {
 			for ( l=0; l<4; l++ ) {
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 4dea2ce1..775567e3 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -884,7 +884,7 @@ UnitCell *cell_transform_rational(UnitCell *cell, RationalMatrix *m)
 	ncen = determine_centering(m, cell_get_centering(cell));
 	cell_set_centering(out, ncen);
 
-	/* FIXME: Update unique axis, lattice type */
+	/* FIXME: Update unique axis, lattice type (GitLab #39) */
 	cell_set_lattice_type(out, L_TRICLINIC);
 	cell_set_unique_axis(out, '?');
 
@@ -972,7 +972,7 @@ UnitCell *cell_transform_rational_inverse(UnitCell *cell, RationalMatrix *m)
 
 	out = cell_transform_gsl_direct(cell, inv);
 
-	/* FIXME: Update centering, unique axis, lattice type */
+	/* FIXME: Update centering, unique axis, lattice type (GitLab #39) */
 
 	gsl_matrix_free(tm);
 	gsl_matrix_free(inv);
diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c
index 19b38607..859ef731 100644
--- a/libcrystfel/src/image-cbf.c
+++ b/libcrystfel/src/image-cbf.c
@@ -635,8 +635,7 @@ int image_cbf_read(struct image *image,
 int image_cbf_read_header_to_cache(struct image *image,
                                    const char *from)
 {
-	/* FIXME: Implementation
-	 * https://gitlab.desy.de/thomas.white/crystfel/-/issues/10 */
+	/* FIXME: Implementation (GitLab #10) */
 	ERROR("Reading headers from CBF files is not currently supported.\n");
 	return 1;
 }
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
index 2995654d..497ce763 100644
--- a/libcrystfel/src/image-hdf5.c
+++ b/libcrystfel/src/image-hdf5.c
@@ -685,7 +685,7 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
 	type = H5Dget_type(dh);
 	class = H5Tget_class(type);
 
-	/* FIXME: Handle strings as well */
+	/* FIXME: Handle strings as well (GitLab #36) */
 	if ( (class != H5T_FLOAT) && (class != H5T_INTEGER) ) {
 		ERROR("Not a floating point or integer value.\n");
 		close_hdf5(fh);
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 10313ca8..7ec79eaf 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -462,7 +462,7 @@ static double get_value(struct image *image, const char *from,
 	if ( image_read_header_float(image, from, &val) == 0 ) {
 		return val;
 	} else {
-		return NAN;  /* FIXME: Use out-of-band flag */
+		return NAN;  /* FIXME: Use out-of-band flag (GitLab #37) */
 	}
 }
 
@@ -767,10 +767,8 @@ static void set_image_parameters(struct image *image,
 
 	image->bw = dtempl->bandwidth;
 
-	/* FIXME: Possibly load spectrum from file */
 	image->spectrum = spectrum_generate_gaussian(image->lambda,
 	                                             image->bw);
-
 }
 
 
diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index 02532103..c56f3ae6 100644
--- a/libcrystfel/src/indexers/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
@@ -29,31 +29,6 @@
  *
  */
 
-/* TODO:
- *
- * Properly read the newmat file (don't use fscanf-- spaces between numers
- *  are not guaranteed)
- *
- * "Success" is indicated by existence of NEWMAT file written by mosflm.
- *  Better to interact with mosflm directly in order to somehow verify success.
- *
- * Investigate how these keywords affect mosflms behavior:
- *
- *  MOSAICITY
- *  DISPERSION
- *  DIVERGENCE
- *  POLARISATION
- *  POSTREF BEAM
- *  POSTREF USEBEAM OFF
- *  PREREFINE ON
- *  EXTRA ON
- *  POSTREF ON
- *
- *  These did not seem to affect the results by my (Rick's) experience, probably
- *  because they are only used conjunction with image intensity data, but it's
- *  worth another look at the documentation.
- */
-
 #include <libcrystfel-config.h>
 
 #include <stdlib.h>
@@ -575,8 +550,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 			                    &a, &b, &c, &alpha, &beta, &gamma);
 			cen = cell_get_centering(mosflm->mp->template);
 			/* Old MOSFLM simply ignores CELL and CENTERING subkeywords.
-			 * So this doesn't do any harm.
-			 * TODO: but still better to show WARNING if MOSFLM is old. */
+			 * So this doesn't do any harm.  */
 			snprintf(tmp, 255, "AUTOINDEX DPS FILE %s IMAGE 1 "
 			         "MAXCELL 1000 REFINE "
 			         "CELL %.1f %.1f %.1f %.1f %.1f %.1f "
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 4b481e93..8ce33083 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -248,8 +248,6 @@ struct TakeTwoCell
 /* Final required step size for refinement of solutions */
 #define ANGLE_CONVERGE_SIZE (deg2rad(0.01))
 
-/* TODO: Multiple lattices */
-
 
 /* ------------------------------------------------------------------------
  * apologetic function
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 45f5f677..b2b6ccfa 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -355,7 +355,7 @@ static void fit_gradient_bg(struct intcontext *ic, struct peak_box *bx)
 	}
 	}
 
-	/* FIXME: SVD is massive overkill here */
+	/* SVD is massive overkill here, but the routine is right there. */
 	ans = solve_svd(v, bx->bgm, NULL, 0);
 	gsl_vector_free(v);
 
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index b871f43a..9b562fb0 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -257,7 +257,7 @@ static int pair_peaks(struct image *image, Crystal *cr,
 		get_detector_pos(refl, &fs, &ss);
 		pd = pow(fs - rps[i].peak->fs, 2.0)
 		   + pow(ss - rps[i].peak->ss, 2.0);
-		if ( pd > 10.0 * 10.0 ) continue; /* FIXME Hardcoded distance */
+		if ( pd > 10.0 * 10.0 ) continue; /* FIXME Hardcoded distance (GitLab #38) */
 
 		rps[n_acc] = rps[i];
 		rps[n_acc].refl = reflection_new(h, k, l);
diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index c354cb19..2b250eff 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -1077,7 +1077,7 @@ int write_to_mtz(RefList *reflist,
 	cellp[4] = rad2deg(be);
 	cellp[5] = rad2deg(ga);
 
-	/* FIXME: Proposed labelling:
+	/* FIXME: Proposed labelling (GitLab #28):
 	 *  title = as above
 	 *  project = basename of folder containing crystfel.project
 	 *  crystal = name of indexing results run
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 47438614..ba6e13c8 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1082,7 +1082,6 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
 					image_set_zero_data(image, st->dtempl_read);
 					image_set_zero_mask(image, st->dtempl_read);
 				}
-				/* FIXME: Maybe arbitrary spectrum from file (?) */
 				image->spectrum = spectrum_generate_gaussian(image->lambda,
 				                                             image->bw);
 				return image;