eduardojsbarroso · Oct 12, 2026 · Oct 9, 2026 · Oct 9, 2026 · Oct 9, 2026 · Oct 9, 2026
diff --git a/clpipe/utils/cosmosis_mcmc_plots.py b/clpipe/utils/cosmosis_mcmc_plots.py
@@ -50,8 +50,16 @@
 import numpy as np
 from astropy.io import fits
 from astropy.table import Table
-from getdist import MCSamples, plots
-from IPython.display import Math, display
+
+# getdist switches matplotlib to Agg on import when it does not recognise the
+# notebook backend (older versions only look for 'ipykern'), which stops the
+# figures from showing inline. Keep the backend that was active before.
+_backend = mpl.get_backend()
+from getdist import MCSamples, plots  # noqa: E402
+if mpl.get_backend() != _backend:
+    plt.switch_backend(_backend)
+
+from IPython.display import Math, display  # noqa: E402
 
 try:
     from cosmosis.postprocessing.inputs import read_input as _cosmosis_read
@@ -75,11 +83,69 @@
     "axes.labelsize":    18,
     "xtick.labelsize":    13,
     "ytick.labelsize":    13,
-    "legend.fontsize":   15,
+    "legend.fontsize":   18,
     "legend.frameon":   False,
+    "legend.handlelength": 3.0,
+    "legend.handleheight": 1.4,
     "figure.dpi":       150,
 }
 
+# ══════════════════════════════════════════════════════════════════════════════
+# Shared style for the paper's line and point figures
+# ══════════════════════════════════════════════════════════════════════════════
+
+# Page widths of the two-column journal layout, in inches. Figures are drawn
+# at the width they are printed at, so font sizes below are the printed sizes.
+TEXT_WIDTH = 7.1
+COLUMN_WIDTH = 3.4
+
+# One color and one marker per richness bin (20-35, 35-70, 70-100, 100-200).
+# Okabe-Ito based, ordered so that no two neighbouring bins merge under
+# deuteranopia, protanopia or tritanopia.
+RICHNESS_COLORS = ["#5E3C99", "#D55E00", "#56B4E9", "#E69F00"]
+RICHNESS_MARKERS = ["o", "s", "^", "D"]
+
+PAPER_FIGURE_RC = {
+    "font.size":           8,
+    "axes.labelsize":      9,
+    "axes.titlesize":      9,
+    "legend.fontsize":     8,
+    "xtick.labelsize":     8,
+    "ytick.labelsize":     8,
+    "axes.linewidth":      0.7,
+    "lines.linewidth":     1.4,
+    "lines.markersize":    4,
+    "legend.framealpha":   0.9,
+    "legend.edgecolor":    "0.8",
+    "savefig.dpi":         300,
+}
+
+
+def use_paper_style():
+    """Apply PAPER_FIGURE_RC to every figure made afterwards in the session."""
+    mpl.rcParams.update(PAPER_FIGURE_RC)
+
+
+def add_grid(ax, which="both"):
+    """Major grid in solid grey and minor grid dotted, dark enough for print."""
+    if which in ("both", "major"):
+        ax.grid(True, which="major", linestyle="-", linewidth=0.6, color="0.70")
+    if which in ("both", "minor"):
+        ax.grid(True, which="minor", linestyle=":", linewidth=0.5, color="0.78")
+    ax.set_axisbelow(True)
+
+
+def richness_label(low, high):
+    """Legend label for a richness bin, e.g. '$20 < \\lambda < 35$'."""
+    return rf"${low:.0f} < \lambda < {high:.0f}$"
+
+
+def thicken_legend_lines(fig, linewidth=2.5):
+    """Thicker line handles in the figure legends, so thin contour styles read in print."""
+    for legend in fig.legends:
+        for line in legend.get_lines():
+            line.set_linewidth(linewidth)
+
 
 @dataclass
 class ChainStyle:
@@ -354,7 +420,7 @@ def _resolve(name: str) -> str:
         g = plots.get_subplot_plotter(width_inch=config.figsize)
         g.settings.axes_fontsize = 13
         g.settings.lab_fontsize = 18
-        g.settings.legend_fontsize = 15
+        g.settings.legend_fontsize = 18
         g.settings.figure_legend_loc = "upper right"
         g.settings.axis_tick_x_rotation = 45
         g.settings.num_plot_contours = 2
@@ -373,6 +439,7 @@ def _resolve(name: str) -> str:
             markers=plot_markers,
             param_limits=config.param_limits,
         )
+        thicken_legend_lines(g.fig)
 
         if multiple_fiducials:
             for marker, style in zip(fiducial_values, styles):

diff --git a/examples/capish_simulation/analysis_summary.ipynb b/examples/capish_simulation/analysis_summary.ipynb
diff --git a/examples/capish_simulation/figures/capish_redmapper.pdf b/examples/capish_simulation/figures/capish_redmapper.pdf
diff --git a/examples/capish_simulation/figures/counts_shear_capish_z0.5_0.6.pdf b/examples/capish_simulation/figures/counts_shear_capish_z0.5_0.6.pdf
diff --git a/examples/capish_simulation/run_in2p3_both_mean/TJPCov.yml b/examples/capish_simulation/run_in2p3_both_mean/TJPCov.yml
@@ -12,7 +12,7 @@ stages:
     nprocess: 1
 inputs:
     fiducial_cosmology: /sps/lsst/groups/clusters/cl_pipeline_project/TXPipe_data/cosmodc2/fiducial_cosmology.yml
-    clusters_sacc_file: ../mock_DC2like_cluster_sacc_mean.sacc
+    clusters_sacc_file: ../../../data/capish_simulation/mock_DC2like_cluster_sacc_mean.sacc
 config: ./config_in2p3_both.yml
 resume: false
 output_dir: ./outputs_both

diff --git a/examples/cosmodc2_redmapper/crow_clcosmo_benchmark.ipynb b/examples/cosmodc2_redmapper/crow_clcosmo_benchmark.ipynb
diff --git a/examples/cosmodc2_redmapper/data_clcosmosim_txpipe.ipynb b/examples/cosmodc2_redmapper/data_clcosmosim_txpipe.ipynb
diff --git a/...dmapper/fiducial_cosmology_analysis/cosmo_0.22_0.7/run_in2p3_both/launch_job_all_in2p3.sh b/...dmapper/fiducial_cosmology_analysis/cosmo_0.22_0.7/run_in2p3_both/launch_job_all_in2p3.sh
@@ -22,4 +22,4 @@ ceci TJPCov.yml
 ceci Firecrown.yml
 
 cd ./outputs_both
-cosmosis sampler_file.ini
+mpirun -n ${SLURM_NTASKS} cosmosis --mpi sampler_file.ini
diff --git a/...dmapper/fiducial_cosmology_analysis/cosmo_0.22_0.9/run_in2p3_both/launch_job_all_in2p3.sh b/...dmapper/fiducial_cosmology_analysis/cosmo_0.22_0.9/run_in2p3_both/launch_job_all_in2p3.sh
@@ -0,0 +1,29 @@
+#!/usr/bin/bash
+#SBATCH --time=25:00:00
+#SBATCH --partition=hpc,lsst
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=80gb
+#SBATCH --ntasks=51
+
+module load conda
+export HDF5_DO_MPI_FILE_SYNC=0
+#export PYTHONPATH=/sps/lsst/groups/clusters/cl_pipeline_project/TXPipe:$PYTHONPATH
+conda activate /sps/lsst/groups/clusters/cl_pipeline_project/conda_envs/txpipe_clp
+export PYTHONPATH=/sps/lsst/users/ebarroso/CLPipe:$PYTHONPATH
+export PYTHONPATH=/sps/lsst/groups/clusters/cl_pipeline_project/TXPipe:$PYTHONPATH
+
+ceci TXPipe.yml
+
+conda deactivate
+conda activate /sps/lsst/groups/clusters/cl_pipeline_project/conda_envs/firecrown_developer_clp
+export PYTHONPATH=/sps/lsst/users/ebarroso/CLPipe:$PYTHONPATH
+
+ceci TJPCov.yml
+ceci Firecrown.yml
+
+cd ./outputs_both
+export OMP_NUM_THREADS=1
+export OPENBLAS_NUM_THREADS=1
+export MKL_NUM_THREADS=1
+export NUMEXPR_NUM_THREADS=1
+mpirun -n ${SLURM_NTASKS} cosmosis --mpi sampler_file.ini
diff --git a/...edmapper/fiducial_cosmology_analysis/cosmo_0.3_0.9/run_in2p3_both/launch_job_all_in2p3.sh b/...edmapper/fiducial_cosmology_analysis/cosmo_0.3_0.9/run_in2p3_both/launch_job_all_in2p3.sh
@@ -22,4 +22,4 @@ ceci TJPCov.yml
 ceci Firecrown.yml
 
 cd ./outputs_both
-cosmosis sampler_file.ini
+mpirun -n ${SLURM_NTASKS} cosmosis --mpi sampler_file.ini
diff --git a/...edmapper/fiducial_cosmology_analysis/cosmo_0.4_0.8/run_in2p3_both/launch_job_all_in2p3.sh b/...edmapper/fiducial_cosmology_analysis/cosmo_0.4_0.8/run_in2p3_both/launch_job_all_in2p3.sh
@@ -22,4 +22,4 @@ ceci TJPCov.yml
 ceci Firecrown.yml
 
 cd ./outputs_both
-cosmosis sampler_file.ini
+mpirun -n ${SLURM_NTASKS} cosmosis --mpi sampler_file.ini
diff --git a/...cosmodc2_redmapper/fiducial_cosmology_analysis/shear_profiles_different_cosmologies.ipynb b/...cosmodc2_redmapper/fiducial_cosmology_analysis/shear_profiles_different_cosmologies.ipynb
diff --git a/examples/cosmodc2_redmapper/figures/10mpc_clpipeline_vs_clcosmo.pdf b/examples/cosmodc2_redmapper/figures/10mpc_clpipeline_vs_clcosmo.pdf
diff --git a/examples/cosmodc2_redmapper/figures/clpipe_vs_payerne.pdf b/examples/cosmodc2_redmapper/figures/clpipe_vs_payerne.pdf
diff --git a/examples/cosmodc2_redmapper/figures/cluster_halo_redshift.pdf b/examples/cosmodc2_redmapper/figures/cluster_halo_redshift.pdf
diff --git a/examples/cosmodc2_redmapper/figures/cosmodc2_contour.png b/examples/cosmodc2_redmapper/figures/cosmodc2_contour.png
diff --git a/examples/cosmodc2_redmapper/figures/counts_vs_richness_with_predictions.pdf b/examples/cosmodc2_redmapper/figures/counts_vs_richness_with_predictions.pdf
diff --git a/examples/cosmodc2_redmapper/figures/delta_sigma_cosmo_comparison.pdf b/examples/cosmodc2_redmapper/figures/delta_sigma_cosmo_comparison.pdf
diff --git a/examples/cosmodc2_redmapper/figures/full_fit_baseline.pdf b/examples/cosmodc2_redmapper/figures/full_fit_baseline.pdf
diff --git a/examples/cosmodc2_redmapper/figures/mass_richness_fiducial.pdf b/examples/cosmodc2_redmapper/figures/mass_richness_fiducial.pdf
diff --git a/examples/cosmodc2_redmapper/figures/mass_richness_pdf.pdf b/examples/cosmodc2_redmapper/figures/mass_richness_pdf.pdf
diff --git a/examples/cosmodc2_redmapper/figures/miscentering.pdf b/examples/cosmodc2_redmapper/figures/miscentering.pdf
diff --git a/examples/cosmodc2_redmapper/figures/precision_plot.pdf b/examples/cosmodc2_redmapper/figures/precision_plot.pdf
diff --git a/examples/cosmodc2_redmapper/figures/shear_profiles_with_predictions.pdf b/examples/cosmodc2_redmapper/figures/shear_profiles_with_predictions.pdf
diff --git a/examples/cosmodc2_redmapper/figures/summary_cosmo.pdf b/examples/cosmodc2_redmapper/figures/summary_cosmo.pdf
diff --git a/examples/cosmodc2_redmapper/figures/summary_tension_cosmo.pdf b/examples/cosmodc2_redmapper/figures/summary_tension_cosmo.pdf
diff --git a/examples/cosmodc2_redmapper/miscentering_fiducial.ipynb b/examples/cosmodc2_redmapper/miscentering_fiducial.ipynb
diff --git a/examples/cosmodc2_redmapper/mor_fiducial.ipynb b/examples/cosmodc2_redmapper/mor_fiducial.ipynb
diff --git a/examples/cosmodc2_redmapper/plot_samples.ipynb b/examples/cosmodc2_redmapper/plot_samples.ipynb