now compiling paper locally using inara and pandoc

.github/workflows/draft-pdf.yml

@@ -1,23 +1,23 @@
-on: [push]
+# on: [push]
 
-jobs:
-  paper:
-    runs-on: ubuntu-latest
-    name: Paper Draft
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Build draft PDF
-        uses: openjournals/openjournals-draft-action@master
-        with:
-          journal: joss
-          # This should be the path to the paper within your repo.
-          paper-path: joss/paper.md
-      - name: Upload
-        uses: actions/upload-artifact@v1
-        with:
-          name: paper
-          # This is the output path where Pandoc will write the compiled
-          # PDF. Note, this should be the same directory as the input
-          # paper.md
-          path: joss/paper.pdf
+# jobs:
+#   paper:
+#     runs-on: ubuntu-latest
+#     name: Paper Draft
+#     steps:
+#       - name: Checkout
+#         uses: actions/checkout@v4
+#       - name: Build draft PDF
+#         uses: openjournals/openjournals-draft-action@master
+#         with:
+#           journal: joss
+#           # This should be the path to the paper within your repo.
+#           paper-path: joss/paper.md
+#       - name: Upload
+#         uses: actions/upload-artifact@v1
+#         with:
+#           name: paper
+#           # This is the output path where Pandoc will write the compiled
+#           # PDF. Note, this should be the same directory as the input
+#           # paper.md
+#           path: joss/paper.pdf

joss/paper.md

@@ -1,5 +1,5 @@
 ---
-title: 'taurex-emcee: A TauREx~3.1 plugin for retrievals using the emcee sampler'
+title: 'taurex-emcee: A TauREx 3.1 plugin for retrievals using the emcee sampler'
 tags:
   - Python
   - astronomy
@@ -13,13 +13,13 @@ authors:
     # equal-contrib: true
     affiliation: "1"
   - name: Quentin Changeat
-    orcid: 
+    orcid: 0000-0001-6516-4493
     affiliation: "2"
   - name: Lorenzo V. Mugnai
-    orcid: 
+    orcid: 0000-0002-9007-9802
     affiliation: "3,4,5"
   - name: Enzo Pascale
-    orcid: 
+    orcid: 0000-0002-3242-8154
     affiliation: "1"            
 affiliations:
  - name: Department of Physics, La Sapienza Università di Roma, Piazzale Aldo Moro 2, Roma, 00185, Italy
@@ -41,21 +41,21 @@ bibliography: paper.bib
 
 <!-- A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience. -->
 
-The `taurex-emcee` plugin is a plugin for the TauREx~3.1 retrieval code that allows users to perform retrievals using the emcee sampler. 
+The `taurex-emcee` plugin is a plugin for the TauREx 3.1 retrieval code that allows users to perform retrievals using the emcee sampler.
+
+Optimized sampling methods are a key component of any retrieval code. Nested samplers are generally considered the most robust sampling method for retrieval of exoplanet atmospheric spectra, and are natively implemented in TauREx 3.1. The estimation of the Bayesian `evidence` is the primary product of nested samplers, whereas the estimation of the Bayesian `posterior` is a by-product. Compared to nested samplers, affine-invariant ensemble samplers sample directly from the Bayesian `posterior`, and therefore the interpretation of the results is more straightforward, even for non-expert users. Moreover, in some instances nested samplers may require to define bespoke priors to ensure that the parameter space is thoroughly explored, whereas affine-invariant ensemble samplers asymptotically sample the entire parameter space. The trade-off being that the latter are more computationally expensive, and the computational time scales much faster with dimensionality.
 
 # Statement of need
 
 <!-- A Statement of need section that clearly illustrates the research purpose of the software and places it in the context of related work. -->
 
-Optimized sampling methods are a key component of any retrieval code. Nested samplers are generally considered the most robust sampling method for retrieval of exoplanet atmospheric spectra, and are natively implemented in TauREx~3.1. The estimation of the Bayesian `evidence` is the primary product of nested samplers, whereas the estimation of the Bayesian `posterior` is a by-product. Compared to nested samplers, affine-invariant ensemble samplers sample directly from the Bayesian `posterior`, and therefore the interpretation of the results is more straightforward, even for non-expert users. Moreover, in some instances nested samplers may require to define bespoke priors to ensure that the parameter space is thoroughly explored, whereas affine-invariant ensemble samplers asymptotically sample the entire parameter space. The trade-off being that the latter are more computationally expensive, and the computational time scales much faster with dimensionality.
-
-The emcee sampler is a popular affine-invariant ensemble sampler that has been used in many fields of astronomy, including exoplanet atmospheric retrievals. The emcee sampler is a popular affine-invariant ensemble sampler that has been used in many fields of astronomy, including exoplanet atmospheric retrievals. The emcee sampler is implemented in the Python package [emcee](https://emcee.readthedocs.io/en/stable/), which is widely used in the astronomy community. However, the emcee sampler is not implemented in the TauREx~3.1 retrieval code, which is a popular open-source code for exoplanet atmospheric retrievals. The `taurex-emcee` plugin implements the emcee sampler in TauREx~3.1, allowing users to perform retrievals using the emcee sampler. The `taurex-emcee` plugin is compatible with the TauREx~3.1 parallelization framework, allowing users to perform parallelized retrievals using the emcee sampler.
+The [emcee](https://emcee.readthedocs.io/en/stable/) sampler is a popular affine-invariant ensemble sampler that is widely used in the astronomy community. However, the emcee sampler is not implemented in the TauREx 3.1 retrieval code, which is a popular open-source code for exoplanet atmospheric retrievals. The `taurex-emcee` plugin implements the emcee sampler in TauREx 3.1, allowing users to perform retrievals using the emcee sampler. The `taurex-emcee` plugin is compatible with the TauREx 3.1 parallelization framework, allowing users to perform parallelized retrievals using the emcee sampler.
 
 # Acknowledgements
 
 <!-- Acknowledgement of any financial support. -->
 
-Andrea Bocchieri and Enzo Pascale acknowledge funding by the Italian Space Agency (ASI) with \ARIEL\ grant n. 2021.5.HH.0.
+Andrea Bocchieri and Enzo Pascale acknowledge funding by the Italian Space Agency (ASI) with `Ariel` grant n. 2021.5.HH.0.
 
 # References