Merge branch 'master' into psconvert-no-file-dup

.github/workflows/build.yml

@@ -63,7 +63,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       - name: Setup vcpkg (Windows)
         run: gh run download -n vcpkg-cache -D C:/vcpkg/installed/

.github/workflows/check-links.yml

@@ -23,11 +23,11 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v4.1.6
+      uses: actions/checkout@v4.2.0
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.10.0
+      uses: lycheeverse/lychee-action@v2.0.2
       with:
         # 429: Too many requests
         args: >
@@ -48,6 +48,7 @@ jobs:
           --exclude ^http://nsis.sourceforge.io
           --exclude ^https://www.ethnologue.com
           --exclude ^https://linux.die.net/man/3/printf
+          --exclude ^https://www.softpedia.com/get/Tweak/Registry-Tweak/EditPath.shtml
           --verbose
           **/*.rst
           **/*.rst_

.github/workflows/ci-caches.yml

@@ -116,7 +116,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       - name: Download GSHHG and DCW datasets
         run: bash ci/download-coastlines.sh
@@ -135,7 +135,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       - name: Install vcpkg libraries
         run: bash ci/install-dependencies-windows.sh

.github/workflows/code-validator.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       - name: Check PSL_strings.h
         run: |

.github/workflows/docker.yml

@@ -92,7 +92,7 @@ jobs:
           fi
 
       - name: Checkout
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       # Fix the git error:
       # "failed to run git: fatal: detected dubious ownership in repository at '/__w/gmt/gmt'"

.github/workflows/docs.yml

@@ -57,7 +57,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       - name: Setup vcpkg (Windows)
         run: gh run download -n vcpkg-cache -D C:/vcpkg/installed/
@@ -134,7 +134,7 @@ jobs:
           echo "${INSTALLDIR}/bin" >> $GITHUB_PATH
 
       - name: Checkout the gh-pages branch in a separate folder
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/dvc-diff.yml

@@ -24,10 +24,10 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4.1.6
+      uses: actions/checkout@v4.2.0
 
     - name: Setup data version control (DVC)
-      uses: iterative/setup-dvc@v1.1.2
+      uses: iterative/setup-dvc@v2
 
     - name: Setup continuous machine learning (CML)
       uses: iterative/setup-cml@v3

.github/workflows/lint-checker.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v4.1.6
+      uses: actions/checkout@v4.2.0
 
     - name: Install cppcheck
       run: |

.github/workflows/release-baseline-images.yml

@@ -20,10 +20,10 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4.1.6
+      uses: actions/checkout@v4.2.0
 
     - name: Setup data version control (DVC)
-      uses: iterative/setup-dvc@v1.1.2
+      uses: iterative/setup-dvc@v2
 
     - name: Pull baseline image data from dvc remote
       run: |

.github/workflows/remind.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4.1.6
+      uses: actions/checkout@v4.2.0
 
     - name: Find and report known failures
       run: |

.github/workflows/tests.yml

@@ -60,7 +60,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.6
+        uses: actions/checkout@v4.2.0
 
       - name: Setup vcpkg (Windows)
         run: gh run download -n vcpkg-cache -D C:/vcpkg/installed/
@@ -173,7 +173,7 @@ jobs:
         if: failure()
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

README.md

@@ -127,9 +127,9 @@ GMT uses (or can access) raster data derived from these sources:
 
 GMT provides several color maps from these sources:
 
-- [SCM (Scientific Color Maps)](http://www.fabiocrameri.ch/visualisation.php)
+- [SCM (Scientific Color Maps)](https://www.fabiocrameri.ch/visualisation.php)
 - [cmocean](https://github.com/kthyng/cmocean-gmt)
-- [cpt-city](http://soliton.vm.bytemark.co.uk/pub/cpt-city/views/totp-cpt.html)
+- [cpt-city](http://www.seaviewsensing.com/pub/cpt-city/)
 - [google](https://ai.googleblog.com/2019/08/turbo-improved-rainbow-colormap-for.html)
 - [matlab](https://www.mathworks.com/help/matlab/colors-1.html)
 - [matplotlib](https://matplotlib.org/stable/tutorials/colors/colormaps.html)

ci/config-gmt-unix.sh

@@ -9,7 +9,6 @@ set (CMAKE_INSTALL_PREFIX "$ENV{INSTALLDIR}")
 set (GSHHG_ROOT "$ENV{COASTLINEDIR}/gshhg")
 set (DCW_ROOT "$ENV{COASTLINEDIR}/dcw")
 
-set (GMT_USE_THREADS TRUE)
 set (GMT_ENABLE_OPENMP TRUE)
 
 # Always use the 'static' data server in CI.
@@ -21,6 +20,12 @@ set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement ${CMAKE_C_FLAGS}")
 set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}")
 EOF
 
+if [ "$EXCLUDE_OPTIONAL" = "true" ]; then
+    echo 'set (GMT_USE_THREADS TRUE)' >> cmake/ConfigUser.cmake
+else
+    echo 'set (GMT_USE_THREADS FALSE)' >> cmake/ConfigUser.cmake
+fi
+
 # Set OpenMP_ROOT so that CMake can find the libomp header and library on macOS
 if [[ "$RUNNER_OS" == "macOS" ]]; then
     echo "set (OpenMP_ROOT $(brew --prefix)/opt/libomp/)" >> cmake/ConfigUser.cmake

ci/install-dependencies-windows.sh

@@ -48,8 +48,8 @@ if [ "$PACKAGE" = "true" ]; then
 fi
 
 # install more packages using conda
-$CONDA\\condabin\\conda.bat update -n base -c conda-forge conda --solver libmamba
-$CONDA\\condabin\\conda.bat install ${conda_packages} -c conda-forge --solver libmamba
+$CONDA\\Scripts\\conda.exe update -n base -c conda-forge conda --solver libmamba
+$CONDA\\Scripts\\conda.exe install ${conda_packages} -c conda-forge --solver libmamba
 echo "$CONDA\\Library\\bin" >> $GITHUB_PATH
 echo "$CONDA\\Scripts" >> $GITHUB_PATH
 

doc/examples/anim06/anim06.sh

@@ -56,7 +56,9 @@ gmt end
 # Build chirp data sets for 1 minute (60 secs); one every 1 ms and one every 0.5 sec as samples
 gmt math -T0/60/0.001 T 2 POW 2 DIV 60 DIV $f MUL 2 MUL PI MUL COS = chirp.txt
 gmt math -T0/60/0.5 -Ca T -C1 2 POW 2 DIV 60 DIV $f MUL 2 MUL PI MUL COS = chirp_samples.txt
+# Build timefile
 gmt math -T0/$frames/1 T $rate DIV = frame_times.txt
+gmt math frame_times.txt -i0,1,1 -C2 2 MUL 60 DIV = frame_times_Hz.txt
 EOF
 # 3. Set up the main frame script
 cat << 'EOF' > main.sh
@@ -83,15 +85,9 @@ gmt begin
 		y=$(gmt math -Q ${MOVIE_COL1} 2 POW 2 DIV 60 DIV $f MUL 2 MUL PI MUL COS =)
 		echo 0 $y | gmt plot -Sc0.5c -Gred
 	fi
-	# Add time counter in upper left corner
-	printf "t = %6.3f s\n" ${MOVIE_COL1} | gmt text -F+f18p,Helvetica-Bold+jTL+cTL -Dj0.3c
-	# Add cycles counter in upper right corner
-	fnow=$(gmt math -Q ${MOVIE_COL1} 60 DIV $f MUL =)
-	printf "f = %6.4f Hz\n" $fnow | gmt text -F+f16p,Helvetica-Bold+jTR+cTR -Dj0.3c
-	# Add frame counter in lower right corner
-	printf "%04d\n" ${MOVIE_FRAME} | gmt text -F+f14p,Helvetica-Bold+jBR+cBR -Dj0.3c
 gmt end
 EOF
 # 4. Run the movie
 source inc.sh
-gmt movie main.sh -Sbpre.sh -CHD -Iinc.sh -Tframe_times.txt -D$rate -Etitle.sh+d6s+fo1s+gwhite -Nanim06 -H8 -Zs -Fmp4 -W -V
+gmt movie main.sh -Sbpre.sh -CHD -Iinc.sh -Tframe_times_Hz.txt -D$rate -Etitle.sh+d6s+fo1s+gwhite -Nanim06 -H8 -Zs -Fmp4 -W -V \
+ -Lf+jBR+f14p,Helvetica-Bold+jBR+o1.3c -Lc1+t"t = %6.3f s"+f18p,Helvetica-Bold+o1.3c -Lc2+t"f = %6.4f Hz"+f16p,Helvetica-Bold+jTR+o1.3c

doc/examples/anim07/anim07.sh

@@ -21,7 +21,7 @@ gmt begin
 	# Extract a topography CPT
 	gmt makecpt -Cdem2 -T0/6000 -H > z.cpt
 	# Get gradients of the relief from N45E
-	gmt grdgradient @earth_relief_06m -Nt1.2 -A45 -Gintens.grd
+	gmt grdgradient @earth_relief_06m_p -Nt1.2 -A45 -Gintens.grd
 gmt end
 EOF
 # 2. Set up main script

doc/examples/anim08/anim08.sh

@@ -38,7 +38,7 @@ gmt begin
 	2018-12-31T	240
 	EOF
     # Get gradients of the relief from N45E
-    gmt grdgradient @earth_relief_02m -Nt1.2 -A45 -Gintens.nc
+    gmt grdgradient @earth_relief_02m_p -Nt1.2 -A45 -Gintens.nc
 	gmt makecpt -Cterra -T-10000/8000 -H > t.cpt
 gmt end
 EOF

doc/examples/anim11/anim11.sh

@@ -21,7 +21,7 @@ gmt begin
   # Make global grid with a smooth 2-degree day/night transition for the 2020 solstice.
   gmt grdmath -Rd -I2m -rp $(gmt solar -C -o0:1 -I+d2020-06-20+z-10) 2 DAYNIGHT = daynight.grd
   # We will create an intensity grid based on a DEM so that we can see structures in the oceans
-  gmt grdgradient @earth_relief_02m -Nt0.75 -A45 -Gintens.grd
+  gmt grdgradient @earth_relief_02m_p -Nt0.75 -A45 -Gintens.grd
   # Make sure our remote files have been downloaded
   gmt which -Ga @earth_day_02m @earth_night_02m
 gmt end

doc/rst/requirements.txt

@@ -6,7 +6,7 @@
 #
 sphinx_rtd_theme==2.0.0
 sphinx-copybutton==0.5.2
-sphinx-design==0.6.0
+sphinx-design==0.6.1
 sphinx-jinja==2.0.2
 sphinx-togglebutton==0.3.2
 sphinxcontrib-youtube==1.4.1

doc/rst/source/batch.rst

@@ -268,7 +268,7 @@ Shell Limitations
 -----------------
 
 As we cannot control how a shell (e.g., bash or csh) implements piping between two processes (it often
-involves a sub-shell), we advice against using commands in your main script that involve piping the result
+involves a sub-shell), we advise against using commands in your main script that involve piping the result
 from one GMT module into another (e.g., gmt blockmean ..... | gmt surface ...).  Because **batch** is running
 many instances of your main script simultaneously, odd things can happen when sub-shells are involved.
 In our experience, piping in the context of batch script may corrupt the GMT history files, resulting in

doc/rst/source/explain_-n_full.rst_

@@ -22,7 +22,8 @@ The following modifiers are supported:
 - **+a** - Switch off antialiasing (where supported) [default uses antialiasing].
 - **+b** - Override boundary conditions used, by appending *g* for geographic, *p* for periodic, or *n* for
   natural boundary conditions. For the latter two you may append **x** or **y** to specify just one direction, otherwise
-  both are assumed.
+  both are assumed. For more information see :ref:`grid-boundary-conditions`.
+
 - **+c** - Clip the interpolated grid to input z-min/z-max [default may exceed limits].
 - **+t** - Control how close to nodes with NaNs the interpolation will go based on *threshold*. A *threshold* of 1.0
   requires all (4 or 16) nodes involved in interpolation to be non-NaN. For example, 0.5 will interpolate about half

doc/rst/source/gallery/ex32.rst

@@ -6,7 +6,7 @@
 In some cases, it is nice to "drape" an arbitrary image over a
 topographic map. We have already seen how to use
 :doc:`image </image>` to plot an image anywhere in
-out plot. But here are aim is different, we want to manipulate an image
+our plot. But here our aim is different, we want to manipulate an image
 to shade it and plot it in 3-D over topography. This example was
 originally created by Stephan Eickschen for a flyer emphasizing the
 historical economical and cultural bond between Brussels, Maastricht and

doc/rst/source/grd2cpt.rst

@@ -59,7 +59,7 @@ z-values. These are the background color (B) assigned to values lower
 than the lowest *z*-value, the foreground color (F) assigned to values
 higher than the highest *z*-value, and the NaN color (N) painted
 wherever values are undefined.  For color tables beyond the
-current GMT offerings, visit `cpt-city <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>`_.
+current GMT offerings, visit `cpt-city <http://www.seaviewsensing.com/pub/cpt-city/>`_.
 
 If the master CPT includes B, F, and N entries, these will be
 copied into the new master file. If not, the parameters

doc/rst/source/grdgradient.rst

@@ -265,7 +265,7 @@ References
 
 Horn, B.K.P., Hill-Shading and the Reflectance Map, Proceedings of the
 IEEE, Vol. 69, No. 1, January 1981, pp. 14-47.
-(http://people.csail.mit.edu/bkph/papers/Hill-Shading.pdf)
+(https://www.researchgate.net/publication/2996084_Hill_shading_and_the_reflectance_map)
 
 See Also
 --------

doc/rst/source/grdmask.rst

@@ -125,13 +125,13 @@ Optional Arguments
 
 **-S**\ *radius*\|\ *xlim*\ /*ylim*
     Set nodes to inside, on edge, or outside depending on their distance
-    to the nearest data point. Nodes within the searsch *radius* [0] from the
+    to the nearest data point. Nodes within the search *radius* [0] from the
     nearest data point are considered inside; append a distance unit
     (see `Units`_). If *radius* is given as **z** then we instead read
-    individual radii from the 3rd input column.  Unless Cartesian data,
+    individual radii from the 3rd input column. Unless Cartesian data,
     specify the unit of these radii by appending it after **-Sz**.
     If |-S| is not set then we consider the input data to define
-    one or more closed polygon(s) instead.  For Cartesian data with
+    one or more closed polygon(s) instead. For Cartesian data with
     different units you can instead append *xlim*\ /*ylim* which will
     perform a rectangular search where all nodes within ±\ *xlim* and
     ±\ *ylim* of a data point will be considered inside.

doc/rst/source/grdmath.rst

@@ -73,7 +73,7 @@ Optional Arguments
 
 .. _-A:
 
-.. |Add_-A| replace:: (|-A| is only relevant to the **LDISTG** operator)
+.. |Add_-A| replace:: (|-A| is only relevant to the **LDISTG** operator).
 .. include:: explain_-A.rst_
 
 .. _-C:
@@ -416,7 +416,7 @@ The following symbols have special meaning:
 +-------------+-------------------------------------------------+
 | **PHI**     | 1.6180339... (golden ratio)                     |
 +-------------+-------------------------------------------------+
-| **EPS_F**   | 1.192092896e-07 (single precision epsilon       |
+| **EPS_F**   | 1.192092896e-07 (single precision epsilon)      |
 +-------------+-------------------------------------------------+
 | **XMIN**    | Minimum *x* value                               |
 +-------------+-------------------------------------------------+
@@ -518,14 +518,16 @@ Notes On Operators
 #. The stack depth limit is hard-wired to 100.
 
 #. All functions expecting a positive radius (e.g., **LOG**, **KEI**,
-   etc.) are passed the absolute value of their argument. (9) The bitwise
-   operators (**BITAND**, **BITLEFT**, **BITNOT**, **BITOR**, **BITRIGHT**,
-   **BITTEST**, and **BITXOR**) convert a grid's single precision values to
-   unsigned 32-bit ints to perform the bitwise operations. Consequently,
-   the largest whole integer value that can be stored in a float grid is
-   2^24 or 16,777,216. Any higher result will be masked to fit in the lower
-   24 bits.  Thus, bit operations are effectively limited to 24 bit.  All
-   bitwise operators return NaN if given NaN arguments or bit-settings <= 0.
+   etc.) are passed the absolute value of their argument. 
+
+#. The bitwise operators (**BITAND**, **BITLEFT**, **BITNOT**, **BITOR**,
+   **BITRIGHT**, **BITTEST**, and **BITXOR**) convert a grid's single
+   precision values to unsigned 32-bit ints to perform the bitwise
+   operations. Consequently, the largest whole integer value that can be
+   stored in a float grid is 2^24 or 16,777,216. Any higher result will be
+   masked to fit in the lower 24 bits. Thus, bit operations are effectively
+   limited to 24 bit. All bitwise operators return NaN if given NaN
+   arguments or bit-settings <= 0.
 
 #. When OpenMP support is compiled in, a few operators will take advantage
    of the ability to spread the load onto several cores.  At present, the

doc/rst/source/makecpt.rst

@@ -47,7 +47,7 @@ You define an equidistant set of contour intervals or pass
 your own z-table or list, and create a new CPT based on an existing master (dynamic)
 CPT. The resulting CPT can be reversed relative to the master
 cpt, and can be made continuous or discrete.  For color tables beyond the
-current GMT offerings, visit `cpt-city <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>`_.
+current GMT offerings, visit `cpt-city <http://www.seaviewsensing.com/pub/cpt-city/>`_.
 
 The CPT includes three additional colors beyond the range of
 z-values. These are the background color (B) assigned to values lower

doc/rst/source/modules.rst

@@ -160,6 +160,7 @@ All modules are requested via a call to the :doc:`gmt` program.
    supplements/seis/meca
    supplements/seis/polar
    supplements/seis/sac
+   supplements/seis/gmtisf
    supplements/seis/grdshake
    supplements/seis/grdvs30
    supplements/spotter/backtracker
@@ -337,6 +338,7 @@ Supplemental Modules
     - :doc:`/supplements/segy/segyz`
     - :doc:`/supplements/seis/coupe`
     - :doc:`/supplements/seis/meca`
+    - :doc:`/supplements/seis/gmtisf`
     - :doc:`/supplements/seis/polar`
     - :doc:`/supplements/seis/sac`
     - :doc:`/supplements/spotter/backtracker`
@@ -749,6 +751,8 @@ seis
 +-----------------------------------+--------------------+
 | :doc:`/supplements/seis/sac`      | |sac_purpose|      |
 +-----------------------------------+--------------------+
+| :doc:`/supplements/seis/gmtisf`   | |gmtisf_purpose|   |
++-----------------------------------+--------------------+
 | :doc:`/supplements/seis/grdshake` | |grdshake_purpose| |
 +-----------------------------------+--------------------+
 | :doc:`/supplements/seis/grdvs30`  | |grdvs30_purpose|  |