Doc update and minor cleanup; add conda package list

Author: oleg-alexandrov

INSTALLGUIDE.rst

@@ -213,7 +213,7 @@ the processing time should go down. Both ``gdalinfo`` and
 Fetching pre-compiled ASP with conda
 ------------------------------------
 
-ASP's official releases can be fetched with ``conda``, for Linux and OSX with the Intel processor. See :numref:`precompiled_binaries` for how other platforms may be handled.
+ASP's official releases can be downloaded with ``conda``, for Linux and OSX with the Intel processor. See :numref:`precompiled_binaries` for how other platforms may be handled.
 
 The latest conda release is version 3.3.0, published on December 30, 2022. See
 :numref:`news` for what changed since then.  The newer functionality
@@ -291,14 +291,42 @@ official release.
 Alternatively, consider using ``mamba`` instead of ``conda``. It is
 must faster though it is not always guaranteed to work. 
 
+Fixes for potential OSX issues
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+On OSX, if an error about ``tbb`` is encountered, run::
+
+    conda activate asp
+    conda install -c usgs-astrogeology -c conda-forge \
+      embree -y --force-reinstall
+
+If the ``ipfind`` (or ``pc_align`` with the option
+``--initial-transform-from-hillshading``, which uses ``ipfind``) fails, try to
+run this tool along the lines of::
+
+    DYLD_LIBRARY_PATH=$HOME/miniconda3/envs/asp/lib ipfind \
+      <other options>
+
+These issues seem to be caused by how conda handles third-party libraries. This
+is not a problem with the binary release (:numref:`precompiled_binaries`) or 
+with conda on Linux.
+
+Post-installation
+~~~~~~~~~~~~~~~~~
+
+Check that the ``stereo`` command can be found as::
+
+    which stereo
+
 If using ISIS, the environmental variable ISISROOT should be set to
 point to this distribution, such as::
 
     export ISISROOT=$HOME/miniconda3/envs/asp
 
-Check that the ``stereo`` command can be found as::
+Also read :numref:`planetary_images` for how to set up ISIS data.
 
-    which stereo
+Using a precise list of packages
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Some variability may exist in the precise dependencies fetched by
 conda. For the record, the full environment for this release can be

conda/asp_3.3.0_linux_env.yaml

@@ -0,0 +1,261 @@
+name: asp
+channels:
+  - nasa-ames-stereo-pipeline
+  - usgs-astrogeology
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_kmp_llvm
+  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_13
+  - ale=0.9.1=py39h7633fee_0
+  - alsa-lib=1.2.7.2=h166bdaf_0
+  - aom=3.5.0=h27087fc_0
+  - armadillo=12.6.1=h0a193a4_0
+  - arpack=3.7.0=hdefa2d7_2
+  - blas=2.117=openblas
+  - blas-devel=3.9.0=17_linux64_openblas
+  - boost=1.72.0=py39ha90915f_1
+  - boost-cpp=1.72.0=h359cf19_6
+  - brotli-python=1.0.9=py39h5a03fae_9
+  - bullet=2.86.1=0
+  - bz2file=0.98=py_0
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.19.1=hd590300_0
+  - ca-certificates=2023.7.22=hbcca054_0
+  - cairo=1.16.0=ha12eb4b_1010
+  - ceres-solver=1.14.0=hf302a74_15
+  - certifi=2023.7.22=pyhd8ed1ab_0
+  - charset-normalizer=3.2.0=pyhd8ed1ab_0
+  - chrpath=0.16=h7f98852_1002
+  - csm=3.0.3.3=hc9558a2_0
+  - cspice=67=h166bdaf_4
+  - curl=7.87.0=h6312ad2_0
+  - cyrus-sasl=2.1.27=h957375c_6
+  - dbus=1.13.6=h5008d03_3
+  - eigen=3.4.0=h00ab1b0_0
+  - elfutils=0.188=hbb17bd0_0
+  - embree=2.17.7=ha770c72_3
+  - expat=2.5.0=hcb278e6_1
+  - ffmpeg=4.4.2=gpl_hbd009f3_109
+  - fftw=3.3.10=nompi_hc118613_108
+  - fgr=isis7=h3fd9d12_0
+  - flann=1.9.1=hfe772e8_1010
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - fontconfig=2.14.2=h14ed4e7_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - freeglut=3.2.2=h9c3ff4c_1
+  - freetype=2.12.1=hca18f0e_1
+  - geoid=1.0_isis7=1
+  - geos=3.9.1=h9c3ff4c_2
+  - geotiff=1.7.1=ha76d385_4
+  - gettext=0.21.1=h27087fc_0
+  - gflags=2.2.2=he1b5a44_1004
+  - giflib=5.2.1=h0b41bf4_3
+  - glib=2.76.4=hfc55251_0
+  - glib-tools=2.76.4=hfc55251_0
+  - glog=0.6.0=h6f12383_0
+  - gmp=6.2.1=h58526e2_0
+  - gnutls=3.7.8=hf3e180e_0
+  - graphite2=1.3.13=h58526e2_1001
+  - gsl=2.6=he838d99_2
+  - gst-plugins-base=1.20.3=h57caac4_2
+  - gstreamer=1.20.3=hd4edc92_2
+  - harfbuzz=4.2.0=h40b6f09_0
+  - hdf5=1.12.1=nompi_h2386368_104
+  - htdp=1.0_isis7=1
+  - icu=69.1=h9c3ff4c_0
+  - idna=3.4=pyhd8ed1ab_0
+  - ilmbase=2.5.5=h780b84a_0
+  - inja=3.3.0=h9c3ff4c_0
+  - isis=8.0.0=np125_0
+  - jama=125=0
+  - jasper=2.0.33=h0ff4b12_1
+  - jemalloc=5.3.0=hcb278e6_0
+  - jpeg=9e=h0b41bf4_3
+  - kakadu=1=0
+  - kernel-headers_linux-64=3.10.0=h4a8ded7_13
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.20.1=hf9c8cef_0
+  - lame=3.100=h166bdaf_1003
+  - laszip=2.1.0_isis7=h3fd9d12_1
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - lerc=4.0.0=h27087fc_0
+  - libarchive=3.5.2=hb890918_3
+  - libblas=3.9.0=17_linux64_openblas
+  - libcblas=3.9.0=17_linux64_openblas
+  - libclang=13.0.1=default_h7634d5b_3
+  - libcurl=7.87.0=h6312ad2_0
+  - libcxx=16.0.6=h00ab1b0_0
+  - libcxxabi=16.0.6=ha770c72_0
+  - libdeflate=1.14=h166bdaf_0
+  - libdrm=2.4.114=h166bdaf_0
+  - libdrm-cos6-x86_64=2.4.65=4
+  - libedit=3.1.20191231=he28a2e2_2
+  - libelas=isis7=h3fd9d12_0
+  - libev=4.33=h516909a_1
+  - libevent=2.1.10=h9b69904_4
+  - libexpat=2.5.0=hcb278e6_1
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=13.1.0=he5830b7_0
+  - libgdal=3.5_isis8=h3fd9d12_0
+  - libgfortran-ng=13.1.0=h69a702a_0
+  - libgfortran5=13.1.0=h15d22d2_0
+  - libglib=2.76.4=hebfc3b9_0
+  - libglu=9.0.0=he1b5a44_1001
+  - libglvnd-cos7-x86_64=1.0.1=h9b0a68f_1105
+  - libhwloc=2.8.0=h32351e8_1
+  - libiconv=1.17=h166bdaf_0
+  - libidn2=2.3.4=h166bdaf_0
+  - libjemalloc=5.3.0=hcb278e6_0
+  - liblapack=3.9.0=17_linux64_openblas
+  - liblapacke=3.9.0=17_linux64_openblas
+  - liblas=1.8.2_isis8=h3fd9d12_0
+  - libllvm13=13.0.1=hf817b99_2
+  - libmicrohttpd=0.9.77=h97afed2_0
+  - libnabo=isis7=h3fd9d12_0
+  - libnghttp2=1.51.0=hdcd2b5c_0
+  - libnsl=2.0.0=h7f98852_0
+  - libntlm=1.4=h7f98852_1002
+  - libogg=1.3.4=h7f98852_1
+  - libopenblas=0.3.23=pthreads_h80387f5_0
+  - libopencv=4.5.5=py39hb0e02d1_7
+  - libopus=1.3.1=h7f98852_1
+  - libpciaccess=0.17=h166bdaf_0
+  - libpng=1.6.39=h753d276_0
+  - libpointmatcher=isis7=h2bc3f7f_0
+  - libpq=14.5=h2baec63_5
+  - libprotobuf=3.19.6=h3eb15da_0
+  - libsqlite=3.42.0=h2797004_0
+  - libssh2=1.10.0=haa6b8db_3
+  - libstdcxx-ng=13.1.0=hfd8a6a1_0
+  - libtasn1=4.19.0=h166bdaf_0
+  - libtiff=4.4.0=h82bc61c_5
+  - libunistring=0.9.10=h7f98852_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libva=2.18.0=h0b41bf4_0
+  - libvorbis=1.3.7=h9c3ff4c_0
+  - libvpx=1.11.0=h9c3ff4c_3
+  - libwebp-base=1.3.1=hd590300_0
+  - libx11-common-cos6-x86_64=1.6.4=4
+  - libx11-cos6-x86_64=1.6.4=4
+  - libxcb=1.13=h7f98852_1004
+  - libxkbcommon=1.0.3=he3ba5ed_0
+  - libxml2=2.9.14=haae042b_4
+  - libzlib=1.2.13=hd590300_5
+  - llvm-openmp=16.0.6=h4dfa4b3_0
+  - lz4-c=1.9.3=h9c3ff4c_1
+  - lzo=2.10=h516909a_1000
+  - mesa-libgl-cos6-x86_64=11.0.7=4
+  - mesalib=23.0.0=h0fe20ba_0
+  - metis=5.1.1=h59595ed_0
+  - mpfr=4.2.0=hb012696_0
+  - multiview=isis8=py39h3fd9d12_0
+  - mysql=8.0.28=h3e2b116_2
+  - mysql-client=8.0.28=hf89ab62_2
+  - mysql-common=8.0.28=haf5c9bc_2
+  - mysql-connector-c=6.1.11=h6eb9d5d_1007
+  - mysql-devel=8.0.28=haf5c9bc_2
+  - mysql-libs=8.0.28=h28c427c_2
+  - mysql-server=8.0.28=hb253900_2
+  - nanoflann=1.4.2=ha770c72_0
+  - ncurses=6.4=hcb278e6_0
+  - nettle=3.8.1=hc379101_1
+  - networkx=3.1=pyhd8ed1ab_0
+  - nlohmann_json=3.11.2=h27087fc_0
+  - nn=1.86.0=h14c3975_2003
+  - nspr=4.35=h27087fc_0
+  - nss=3.89=he45b914_0
+  - numpy=1.25.2=py39h6183b62_0
+  - openblas=0.3.23=pthreads_h855a84d_0
+  - opencv=4.5.5=py39hf3d152e_7
+  - openexr=2.5.5=hf817b99_0
+  - openh264=2.3.1=hcb278e6_2
+  - openjpeg=2.3.0=hf38bd82_1003
+  - openssl=1.1.1v=hd590300_0
+  - p11-kit=0.24.1=hc5aa10d_0
+  - packaging=23.1=pyhd8ed1ab_0
+  - parallel=20230722=ha770c72_0
+  - pbzip2=1.1.13=0
+  - pcl=1.11.1=h05311af_1
+  - pcre2=10.40=hc3806b6_0
+  - perl=5.32.1=4_hd590300_perl5
+  - pip=23.2.1=pyhd8ed1ab_0
+  - pixman=0.40.0=h36c2ea0_0
+  - platformdirs=3.10.0=pyhd8ed1ab_0
+  - pooch=1.7.0=pyha770c72_3
+  - proj=9.1.0=h93bde94_0
+  - protobuf=3.19.6=py39h227be39_0
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pvl=1.3.2=pyhd8ed1ab_0
+  - py-opencv=4.5.5=py39hef51801_7
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.9.15=h47a2c10_0_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python_abi=3.9=3_cp39
+  - pytz=2023.3=pyhd8ed1ab_0
+  - pyyaml=6.0=py39hb9d737c_5
+  - qhull=2020.2=h4bd325d_2
+  - qt=5.12.9=h1304e3e_6
+  - qwt=6.2.0=hb19a904_2
+  - rapidjson=1.1.0=he1b5a44_1002
+  - rclone=1.63.1=h519d9b9_0
+  - readline=8.2=h8228510_1
+  - requests=2.31.0=pyhd8ed1ab_0
+  - rocksdb=6.13.3=hda8cf21_2
+  - s2p-subset=isis7=h3fd9d12_0
+  - scipy=1.11.2=py39h6183b62_0
+  - setuptools=68.1.2=pyhd8ed1ab_0
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.1.10=h9fff704_0
+  - spiceypy=5.1.2=pyhd8ed1ab_0
+  - sqlite=3.42.0=h2c6b66d_0
+  - stereo-pipeline=3.3.0=h3fd9d12_0
+  - suitesparse=5.10.1=h9e50725_1
+  - superlu=5.2.2=h00795ac_0
+  - svt-av1=1.3.0=h27087fc_0
+  - sysroot_linux-64=2.17=h4a8ded7_13
+  - tbb=2021.7.0=h924138e_1
+  - tbb-devel=2021.7.0=h924138e_1
+  - tk=8.6.12=h27826a3_0
+  - tnt=126=0
+  - typing-extensions=4.7.1=hd8ed1ab_0
+  - typing_extensions=4.7.1=pyha770c72_0
+  - tzdata=2023c=h71feb2d_0
+  - urllib3=2.0.4=pyhd8ed1ab_0
+  - usgscsm=1.7.0=h00ab1b0_1
+  - visionworkbench=3.3.0=h3fd9d12_0
+  - wheel=0.41.1=pyhd8ed1ab_0
+  - x264=1!164.3095=h166bdaf_2
+  - x265=3.5=h924138e_3
+  - xerces-c=3.2.3=h8ce2273_4
+  - xorg-damageproto=1.2.1=h7f98852_1002
+  - xorg-fixesproto=5.0=h7f98852_1002
+  - xorg-glproto=1.4.17=h7f98852_1002
+  - xorg-inputproto=2.3.2=h7f98852_1002
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.1.1=hd590300_0
+  - xorg-libsm=1.2.4=h7391055_0
+  - xorg-libx11=1.8.4=h0b41bf4_0
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdamage=1.1.5=h7f98852_1
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h0b41bf4_2
+  - xorg-libxfixes=5.0.3=h7f98852_1004
+  - xorg-libxi=1.7.10=h7f98852_0
+  - xorg-libxrandr=1.5.2=h7f98852_1
+  - xorg-libxrender=0.9.10=h7f98852_1003
+  - xorg-randrproto=1.5.0=h7f98852_1001
+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-util-macros=1.19.3=h7f98852_0
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
+  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
+  - xz=5.2.6=h166bdaf_0
+  - yaml=0.2.5=h7f98852_2
+  - zlib=1.2.13=hd590300_5
+  - zstd=1.5.2=hfc55251_7