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Merge branch 'master' of https://github.com/vincefn/objcryst into upstream-objcryst
2 parents 59442de + 71e6685 commit b7dece2

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‎ChangeLog.txt

+9
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,12 @@
1+
#### 2022.2 (XX 2022)
2+
NEW FEATURES
3+
* The macOS image is now a universal binary for Apple Silicon (ARM64)
4+
and X86_64 machines
5+
6+
IMPROVEMENTS
7+
* the list of HKL reflections will now be more automatically be re-generated
8+
when the spacegroup changes or the lattice parameters change by more than 0.5%
9+
110
#### 2022.1 (May 2022)
211
NEW FEATURES
312
* Add cylindrical absorption correction (mu*R)

‎Fox/Fox.xcodeproj/project.pbxproj

+82-23
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
archiveVersion = 1;
44
classes = {
55
};
6-
objectVersion = 46;
6+
objectVersion = 53;
77
objects = {
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99
/* Begin PBXBuildFile section */
@@ -153,10 +153,10 @@
153153
BF69C4D9124F8C310035CF57 /* WXGridWindow.cpp in Sources */ = {isa = PBXBuildFile; fileRef = BF69C4D0124F8C310035CF57 /* WXGridWindow.cpp */; };
154154
BF92D5CF259F2D50005FD5D7 /* Undo.cpp in Sources */ = {isa = PBXBuildFile; fileRef = BF92D5CE259F2D4F005FD5D7 /* Undo.cpp */; };
155155
BFCB29CD258F7484008A8CCB /* include.h in Headers */ = {isa = PBXBuildFile; fileRef = BFCB29CC258F7484008A8CCB /* include.h */; };
156-
BFE729E4243A6A6D00BABE40 /* libwx_osx_cocoau_gl-3.1.a in Frameworks */ = {isa = PBXBuildFile; fileRef = BFF7D0BF1478047800799F7A /* libwx_osx_cocoau_gl-3.1.a */; };
157-
BFE729E5243A6A7000BABE40 /* libwx_osx_cocoau-3.1.a in Frameworks */ = {isa = PBXBuildFile; fileRef = BFF7D0C01478047800799F7A /* libwx_osx_cocoau-3.1.a */; };
158-
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159-
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156+
BFE729E4243A6A6D00BABE40 /* libwx_osx_cocoau_gl-3.2.a in Frameworks */ = {isa = PBXBuildFile; fileRef = BFF7D0BF1478047800799F7A /* libwx_osx_cocoau_gl-3.2.a */; };
157+
BFE729E5243A6A7000BABE40 /* libwx_osx_cocoau-3.2.a in Frameworks */ = {isa = PBXBuildFile; fileRef = BFF7D0C01478047800799F7A /* libwx_osx_cocoau-3.2.a */; };
158+
BFE729E6243A6A7300BABE40 /* libwxjpeg-3.2.a in Frameworks */ = {isa = PBXBuildFile; fileRef = BFF7D0C11478047800799F7A /* libwxjpeg-3.2.a */; };
159+
BFE729E7243A6A7600BABE40 /* libwxpng-3.2.a in Frameworks */ = {isa = PBXBuildFile; fileRef = BFF7D0C21478047800799F7A /* libwxpng-3.2.a */; };
160160
BFFB474E0E5E0E620027591E /* wxLSQ.cpp in Sources */ = {isa = PBXBuildFile; fileRef = BFFB474D0E5E0E620027591E /* wxLSQ.cpp */; };
161161
BFFCCB670890296D00044EBA /* bandmat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = BFFCCB660890296D00044EBA /* bandmat.cpp */; };
162162
BFFCCBA0089029F400044EBA /* cholesky.cpp in Sources */ = {isa = PBXBuildFile; fileRef = BFFCCB6A089029F400044EBA /* cholesky.cpp */; };
@@ -359,10 +359,10 @@
359359
BF92D5CE259F2D4F005FD5D7 /* Undo.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = Undo.cpp; path = ../ObjCryst/ObjCryst/Undo.cpp; sourceTree = "<group>"; };
360360
BFCB29CC258F7484008A8CCB /* include.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = include.h; path = ../newmat/include.h; sourceTree = "<group>"; };
361361
BFE6AC680B886ACA007AFBA8 /* Indexing.cpp */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; name = Indexing.cpp; path = ../ObjCryst/ObjCryst/Indexing.cpp; sourceTree = SOURCE_ROOT; };
362-
BFF7D0BF1478047800799F7A /* libwx_osx_cocoau_gl-3.1.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwx_osx_cocoau_gl-3.1.a"; path = "../static-libs/lib/libwx_osx_cocoau_gl-3.1.a"; sourceTree = "<group>"; };
363-
BFF7D0C01478047800799F7A /* libwx_osx_cocoau-3.1.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwx_osx_cocoau-3.1.a"; path = "../static-libs/lib/libwx_osx_cocoau-3.1.a"; sourceTree = "<group>"; };
364-
BFF7D0C11478047800799F7A /* libwxjpeg-3.1.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwxjpeg-3.1.a"; path = "../static-libs/lib/libwxjpeg-3.1.a"; sourceTree = "<group>"; };
365-
BFF7D0C21478047800799F7A /* libwxpng-3.1.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwxpng-3.1.a"; path = "../static-libs/lib/libwxpng-3.1.a"; sourceTree = "<group>"; };
362+
BFF7D0BF1478047800799F7A /* libwx_osx_cocoau_gl-3.2.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwx_osx_cocoau_gl-3.2.a"; path = "../static-libs/lib/libwx_osx_cocoau_gl-3.2.a"; sourceTree = "<group>"; };
363+
BFF7D0C01478047800799F7A /* libwx_osx_cocoau-3.2.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwx_osx_cocoau-3.2.a"; path = "../static-libs/lib/libwx_osx_cocoau-3.2.a"; sourceTree = "<group>"; };
364+
BFF7D0C11478047800799F7A /* libwxjpeg-3.2.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwxjpeg-3.2.a"; path = "../static-libs/lib/libwxjpeg-3.2.a"; sourceTree = "<group>"; };
365+
BFF7D0C21478047800799F7A /* libwxpng-3.2.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = "libwxpng-3.2.a"; path = "../static-libs/lib/libwxpng-3.2.a"; sourceTree = "<group>"; };
366366
BFFB474D0E5E0E620027591E /* wxLSQ.cpp */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; name = wxLSQ.cpp; path = ../ObjCryst/wxCryst/wxLSQ.cpp; sourceTree = SOURCE_ROOT; };
367367
BFFCCB5D089028E500044EBA /* libnewmat.a */ = {isa = PBXFileReference; explicitFileType = archive.ar; includeInIndex = 0; path = libnewmat.a; sourceTree = BUILT_PRODUCTS_DIR; };
368368
BFFCCB660890296D00044EBA /* bandmat.cpp */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; name = bandmat.cpp; path = ../newmat/bandmat.cpp; sourceTree = "<group>"; };
@@ -1948,18 +1948,18 @@
19481948
BF1DE1130D228E6100A3939D /* AGL.framework in Frameworks */,
19491949
BF5EBF13283F8CB2000D09FE /* QuartzCore.framework in Frameworks */,
19501950
BF1DE1140D228E6100A3939D /* Carbon.framework in Frameworks */,
1951-
BFE729E6243A6A7300BABE40 /* libwxjpeg-3.1.a in Frameworks */,
1951+
BFE729E6243A6A7300BABE40 /* libwxjpeg-3.2.a in Frameworks */,
19521952
BF1DE1150D228E6100A3939D /* System.framework in Frameworks */,
19531953
BF1DE1160D228E6100A3939D /* IOKit.framework in Frameworks */,
1954-
BFE729E7243A6A7600BABE40 /* libwxpng-3.1.a in Frameworks */,
1954+
BFE729E7243A6A7600BABE40 /* libwxpng-3.2.a in Frameworks */,
19551955
BF1DE1170D228E6100A3939D /* OpenGL.framework in Frameworks */,
19561956
BF1DE1180D228E6100A3939D /* AppKit.framework in Frameworks */,
19571957
BF1DE1190D228E6100A3939D /* GLUT.framework in Frameworks */,
19581958
BF1DE11A0D228E6100A3939D /* WebKit.framework in Frameworks */,
19591959
BF1DE1110D228E5D00A3939D /* libcctbx.a in Frameworks */,
19601960
BF1DE1120D228E5D00A3939D /* libnewmat.a in Frameworks */,
1961-
BFE729E5243A6A7000BABE40 /* libwx_osx_cocoau-3.1.a in Frameworks */,
1962-
BFE729E4243A6A6D00BABE40 /* libwx_osx_cocoau_gl-3.1.a in Frameworks */,
1961+
BFE729E5243A6A7000BABE40 /* libwx_osx_cocoau-3.2.a in Frameworks */,
1962+
BFE729E4243A6A6D00BABE40 /* libwx_osx_cocoau_gl-3.2.a in Frameworks */,
19631963
BF1DE1240D228EA500A3939D /* libfftw3f.a in Frameworks */,
19641964
);
19651965
runOnlyForDeploymentPostprocessing = 0;
@@ -2273,10 +2273,10 @@
22732273
BFFCCB4F089028D300044EBA = {
22742274
isa = PBXGroup;
22752275
children = (
2276-
BFF7D0BF1478047800799F7A /* libwx_osx_cocoau_gl-3.1.a */,
2277-
BFF7D0C01478047800799F7A /* libwx_osx_cocoau-3.1.a */,
2278-
BFF7D0C11478047800799F7A /* libwxjpeg-3.1.a */,
2279-
BFF7D0C21478047800799F7A /* libwxpng-3.1.a */,
2276+
BFF7D0BF1478047800799F7A /* libwx_osx_cocoau_gl-3.2.a */,
2277+
BFF7D0C01478047800799F7A /* libwx_osx_cocoau-3.2.a */,
2278+
BFF7D0C11478047800799F7A /* libwxjpeg-3.2.a */,
2279+
BFF7D0C21478047800799F7A /* libwxpng-3.2.a */,
22802280
BF1DE1230D228EA500A3939D /* libfftw3f.a */,
22812281
BF36112F0BD6E409000C0EE9 /* WebKit.framework */,
22822282
BF36112B0BD6E3F5000C0EE9 /* GLUT.framework */,
@@ -4591,13 +4591,15 @@
45914591
BFFCCB51089028D300044EBA /* Project object */ = {
45924592
isa = PBXProject;
45934593
attributes = {
4594+
BuildIndependentTargetsInParallel = YES;
45944595
LastUpgradeCheck = 0710;
45954596
};
45964597
buildConfigurationList = BFFCCB52089028D300044EBA /* Build configuration list for PBXProject "Fox" */;
45974598
compatibilityVersion = "Xcode 3.2";
45984599
developmentRegion = English;
45994600
hasScannedForEncodings = 0;
46004601
knownRegions = (
4602+
English,
46014603
en,
46024604
);
46034605
mainGroup = BFFCCB4F089028D300044EBA;
@@ -4836,11 +4838,11 @@
48364838
GCC_VERSION = "";
48374839
HEADER_SEARCH_PATHS = (
48384840
"$(SRCROOT)/../static-libs/include",
4839-
"$(SRCROOT)/../static-libs/include/wx-3.1",
4840-
"$(SRCROOT)/../static-libs/lib/wx/include/osx_cocoa-unicode-static-3.1",
4841+
"$(SRCROOT)/../static-libs/include/wx-3.2",
48414842
"$(SRCROOT)/../ObjCryst",
48424843
"$(SRCROOT)/../cctbx/include",
48434844
"$(SRCROOT)/../",
4845+
"$(SRCROOT)/../static-libs/lib/wx/include/osx_cocoa-unicode-static-3.2",
48444846
);
48454847
INFOPLIST_FILE = "Fox-Info.plist";
48464848
INSTALL_PATH = "$(HOME)/Applications";
@@ -4864,6 +4866,35 @@
48644866
"-D__FOX_COD__",
48654867
"-DwxDEBUG_LEVEL=0",
48664868
);
4869+
"OTHER_CFLAGS[arch=arm64]" = (
4870+
"-D_FILE_OFFSET_BITS=64",
4871+
"-D_LARGE_FILES",
4872+
"-D__WXMAC__",
4873+
"-DHAVE_FFTW",
4874+
"-D__WX__CRYST__",
4875+
"-DOBJCRYST_GL",
4876+
"-DHAVE_GLUT",
4877+
"-D__WXOSX__",
4878+
"-D__WXOSX_COCOA__",
4879+
"-D__FOX_COD__",
4880+
"-DwxDEBUG_LEVEL=0",
4881+
);
4882+
"OTHER_CFLAGS[arch=x86_64]" = (
4883+
"-DUSE_SSE2",
4884+
"-DHAVE_SSE_MATHFUN",
4885+
"-D_FILE_OFFSET_BITS=64",
4886+
"-D_LARGE_FILES",
4887+
"-D__WXMAC__",
4888+
"-DHAVE_FFTW",
4889+
"-D__WX__CRYST__",
4890+
"-DOBJCRYST_GL",
4891+
"-DHAVE_GLUT",
4892+
"-D__WXOSX__",
4893+
"-D__WXOSX_COCOA__",
4894+
"-D__FOX_COD__",
4895+
"-DwxDEBUG_LEVEL=0",
4896+
);
4897+
"OTHER_CPLUSPLUSFLAGS[arch=*]" = "$(OTHER_CFLAGS)";
48674898
OTHER_LDFLAGS = (
48684899
"-framework",
48694900
Foundation,
@@ -4901,7 +4932,7 @@
49014932
GCC_STRICT_ALIASING = NO;
49024933
"INSTALL_PATH[sdk=*]" = "";
49034934
MACOSX_DEPLOYMENT_TARGET = 10.10;
4904-
ONLY_ACTIVE_ARCH = YES;
4935+
ONLY_ACTIVE_ARCH = NO;
49054936
"OTHER_CPLUSPLUSFLAGS[arch=*]" = (
49064937
"$(OTHER_CFLAGS)",
49074938
"-D__DEBUG__",
@@ -5012,11 +5043,11 @@
50125043
HEADER_SEARCH_PATHS = (
50135044
"$(SRCROOT)/../",
50145045
"$(SRCROOT)/../static-libs/include",
5015-
"$(SRCROOT)/../static-libs/include/wx-3.1",
5016-
"$(SRCROOT)/../static-libs/lib/wx/include/osx_cocoa-unicode-static-3.1",
5046+
"$(SRCROOT)/../static-libs/include/wx-3.2",
50175047
"$(SRCROOT)/../ObjCryst",
50185048
"$(SRCROOT)/../cctbx/include",
50195049
"$(SRCROOT)/../cctbx/scitbx/include",
5050+
"$(SRCROOT)/../static-libs/lib/wx/include/osx_cocoa-unicode-static-3.2",
50205051
);
50215052
INFOPLIST_FILE = "Fox-Info.plist";
50225053
INSTALL_PATH = "$(HOME)/Applications";
@@ -5040,6 +5071,34 @@
50405071
"-D__FOX_COD__",
50415072
"-DwxDEBUG_LEVEL=0",
50425073
);
5074+
"OTHER_CFLAGS[arch=arm64]" = (
5075+
"-D_FILE_OFFSET_BITS=64",
5076+
"-D_LARGE_FILES",
5077+
"-D__WXMAC__",
5078+
"-DHAVE_FFTW",
5079+
"-D__WX__CRYST__",
5080+
"-DOBJCRYST_GL",
5081+
"-DHAVE_GLUT",
5082+
"-D__WXOSX__",
5083+
"-D__WXOSX_COCOA__",
5084+
"-D__FOX_COD__",
5085+
"-DwxDEBUG_LEVEL=0",
5086+
);
5087+
"OTHER_CFLAGS[arch=x86_64]" = (
5088+
"-DUSE_SSE2",
5089+
"-DHAVE_SSE_MATHFUN",
5090+
"-D_FILE_OFFSET_BITS=64",
5091+
"-D_LARGE_FILES",
5092+
"-D__WXMAC__",
5093+
"-DHAVE_FFTW",
5094+
"-D__WX__CRYST__",
5095+
"-DOBJCRYST_GL",
5096+
"-DHAVE_GLUT",
5097+
"-D__WXOSX__",
5098+
"-D__WXOSX_COCOA__",
5099+
"-D__FOX_COD__",
5100+
"-DwxDEBUG_LEVEL=0",
5101+
);
50435102
OTHER_LDFLAGS = (
50445103
"-framework",
50455104
Foundation,
@@ -5158,7 +5217,7 @@
51585217
GCC_OPTIMIZATION_LEVEL = 3;
51595218
GCC_STRICT_ALIASING = NO;
51605219
MACOSX_DEPLOYMENT_TARGET = 10.10;
5161-
ONLY_ACTIVE_ARCH = YES;
5220+
ONLY_ACTIVE_ARCH = NO;
51625221
OTHER_CFLAGS = "";
51635222
SKIP_INSTALL = YES;
51645223
};

‎Fox/doc/.readthedocs.yaml

+15
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
version: 2
2+
3+
build:
4+
os: "ubuntu-22.04"
5+
tools:
6+
python: "3.12"
7+
8+
sphinx:
9+
configuration: Fox/doc/source/conf.py
10+
11+
# Python requirements to build your documentation
12+
# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
13+
python:
14+
install:
15+
- requirements: Fox/doc/requirements.txt

‎Fox/doc/Makefile

+20
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,20 @@
1+
# Minimal makefile for Sphinx documentation
2+
#
3+
4+
# You can set these variables from the command line, and also
5+
# from the environment for the first two.
6+
SPHINXOPTS ?=
7+
SPHINXBUILD ?= sphinx-build
8+
SOURCEDIR = source
9+
BUILDDIR = build
10+
11+
# Put it first so that "make" without argument is like "make help".
12+
help:
13+
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
14+
15+
.PHONY: help Makefile
16+
17+
# Catch-all target: route all unknown targets to Sphinx using the new
18+
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
19+
%: Makefile
20+
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎Fox/doc/make.bat

+35
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
@ECHO OFF
2+
3+
pushd %~dp0
4+
5+
REM Command file for Sphinx documentation
6+
7+
if "%SPHINXBUILD%" == "" (
8+
set SPHINXBUILD=sphinx-build
9+
)
10+
set SOURCEDIR=source
11+
set BUILDDIR=build
12+
13+
%SPHINXBUILD% >NUL 2>NUL
14+
if errorlevel 9009 (
15+
echo.
16+
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
17+
echo.installed, then set the SPHINXBUILD environment variable to point
18+
echo.to the full path of the 'sphinx-build' executable. Alternatively you
19+
echo.may add the Sphinx directory to PATH.
20+
echo.
21+
echo.If you don't have Sphinx installed, grab it from
22+
echo.https://www.sphinx-doc.org/
23+
exit /b 1
24+
)
25+
26+
if "%1" == "" goto help
27+
28+
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
29+
goto end
30+
31+
:help
32+
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
33+
34+
:end
35+
popd

‎Fox/doc/requirements.txt

+1
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
pydata-sphinx-theme

‎Fox/doc/source/_static/Fox.png

64.7 KB
Loading

‎Fox/doc/source/_static/css/custom.css

+18
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
/*default is 60em*/
2+
.bd-main .bd-content .bd-article-container {
3+
max-width: 120em;
4+
}
5+
6+
/* default is 88rem*/
7+
.bd-page-width {
8+
max-width: 120em;
9+
}
10+
11+
/* Larger header/navbar for Fox logo*/
12+
.navbar-brand img{
13+
height: auto;
14+
}
15+
16+
.navbar {
17+
height: 6em;
18+
}

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