Fix pre review comments

.github/workflows/draft-pdf.yml

@@ -28,25 +28,4 @@ jobs:
           # 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: paper/paper.pdf
-      - name: Create release
-        if: github.event_name == 'push'
-        uses: rymndhng/release-on-push-action@master
-        id: release
-        with:
-          bump_version_scheme: patch
-          tag_prefix: v
-          release_body: ""
-          use_github_release_notes: true
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Upload PDF to release
-        if: github.event_name == 'push'
-        uses: svenstaro/upload-release-action@v2
-        with:
-          repo_token: ${{ secrets.GITHUB_TOKEN }}
-          file: paper/paper.pdf
-          asset_name: joss-draft.pdf
-          tag: ${{ steps.release.outputs.tag_name }}
-          overwrite: true
-          body: ""
+          path: paper/paper.pdf

.github/workflows/wordcount.yml

@@ -0,0 +1,43 @@
+name: Word Count
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+permissions:
+  contents: read
+  pull-requests: write
+  issues: write
+
+jobs:
+  count-words:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Install Pandoc
+        run: sudo apt-get update && sudo apt-get install -y pandoc
+
+      - name: Count words in paper.md
+        id: wordcount
+        run: |
+          COUNT=$(pandoc paper/paper.md -t plain | wc -w)
+          echo "count=$COUNT" >> $GITHUB_OUTPUT
+          echo "📝 JOSS Word Count: $COUNT words"
+          if [ "$COUNT" -gt 1000 ]; then
+            echo "::warning title=JOSS Word Count::Paper exceeds 1000 words ($COUNT)."
+          fi
+
+      - name: Comment on PR with word count
+        if: github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: joss-wordcount
+          message: |
+            📝 **JOSS Word Count**
+
+            The current word count for `paper.md` is **${{ steps.wordcount.outputs.count }}** words.
+
+            _(JOSS recommends 250-1000 words for the main text.)_

paper/examples/Benchmark.tex

@@ -1,13 +1,9 @@
-\begin{tabular}{lcrrrrr}
+\begin{tabular}{llrrrrr}
   \hline
-  \textbf{Method} & \textbf{Status} & \textbf{$t$($s$)} & \textbf{$\#f$} & \textbf{$\#\nabla f$} & \textbf{$\#prox$} & \textbf{Objective} \\\hline
-  TR (LSR1, SVM) & first\_order & 3.9349 & 347 & 291 & 4037 & 179.837 \\
-  R2N (LSR1, SVM) & first\_order & 1.9511 & 185 & 101 & 27932 & 192.493 \\
-  LM (SVM) & first\_order & 19.7826 & 6 & 2876 & 1001 & 201.186 \\
-  LMTR (SVM) & first\_order & 12.4967 & 11 & 1614 & 432 & 188.274 \\
+  Method & Status & $t$($s$) & $\#f$ & $\#\nabla f$ & $\#prox$ & Objective \\\hline
+  TR & first\_order & 3.9349 & 347 & 291 & 4037 & 179.837 \\
+  R2N & first\_order & 1.9511 & 185 & 101 & 27932 & 192.493 \\
+  LM & first\_order & 19.7826 & 6 & 2876 & 1001 & 201.186 \\
+  LMTR & first\_order & 12.4967 & 11 & 1614 & 432 & 188.274 \\
   \hline
-  TR (LBFGS, NNMF) & first\_order & 0.1014 & 42 & 40 & 3160 & 976.06 \\
-  R2N (LBFGS, NNMF) & first\_order & 0.4913 & 169 & 107 & 17789 & 411.727 \\
-  LM (NNMF) & first\_order & 0.1157 & 14 & 7042 & 2601 & 131.184 \\
-  LMTR (NNMF) & first\_order & 0.0697 & 9 & 4066 & 1435 & 131.186 \\\hline
 \end{tabular}

paper/paper.bib

@@ -1,7 +1,7 @@
 @Article{         aravkin-baraldi-orban-2022,
   Author        = {A. Y. Aravkin and R. Baraldi and D. Orban},
   Title         = {A Proximal Quasi-{N}ewton Trust-Region Method for Nonsmooth Regularized Optimization},
-  Journal       = siopt,
+  Journal       = {SIAM J. Optim.},
   Year          = 2022,
   Volume        = 32,
   Number        = 2,
@@ -12,7 +12,7 @@ @Article{         aravkin-baraldi-orban-2022
 @Article{         aravkin-baraldi-orban-2024,
   Author        = {A. Y. Aravkin and R. Baraldi and D. Orban},
   Title         = {A {L}evenberg–{M}arquardt Method for Nonsmooth Regularized Least Squares},
-  Journal       = sisc,
+  Journal       = {SIAM J. Sci. Comput.},
   Year          = 2024,
   Volume        = 46,
   Number        = 4,
@@ -23,7 +23,7 @@ @Article{         aravkin-baraldi-orban-2024
 @Software{        leconte_linearoperators_jl_linear_operators_2023,
   Author        = {Leconte, Geoffroy and Orban, Dominique and Soares Siqueira, Abel and contributors},
   license       = {MPL-2.0},
-  Title         = {{LinearOperators.jl: Linear Operators for Julia}},
+  Title         = {{LinearOperators.jl}: Linear Operators for Julia},
   url           = {https://github.com/JuliaSmoothOptimizers/LinearOperators.jl},
   version       = {2.6.0},
   Year          = 2023,
@@ -32,34 +32,33 @@ @Software{        leconte_linearoperators_jl_linear_operators_2023
 @Article{         leconte-orban-2023,
   Author        = {G. Leconte and D. Orban},
   Title         = {The Indefinite Proximal Gradient Method},
-  Journal       = coap,
+  Journal       = {Comput. Optim. Appl.},
   Year          = 2025,
   Volume        = 91,
   Number        = 2,
-  Pages         = 861--903,
+  Pages         = {861--903},
   doi           = {10.1007/s10589-024-00604-5},
 }
 
 @TechReport{      leconte-orban-2023-2,
   Author        = {G. Leconte and D. Orban},
   Title         = {Complexity of trust-region methods with unbounded {H}essian approximations for smooth and nonsmooth optimization},
-  Institution   = gerad,
+  Institution   = {GERAD},
   Year          = 2023,
   Type          = {Cahier},
   Number        = {G-2023-65},
-  Address       = gerad-address,
+  Address       = {Montr\'eal, QC, Canada},
   url           = {https://www.gerad.ca/fr/papers/G-2023-65},
 }
 
 @TechReport{      diouane-habiboullah-orban-2024,
   Author        = {Youssef Diouane and Mohamed Laghdaf Habiboullah and Dominique Orban},
-  Title         = {A proximal modified quasi-Newton method for nonsmooth regularized optimization},
+  Title         = {A proximal modified quasi-{N}ewton method for nonsmooth regularized optimization},
   Institution   = {GERAD},
   Year          = 2024,
   Type          = {Cahier},
   Number        = {G-2024-64},
   Address       = {Montr\'eal, Canada},
-  doi           = {10.48550/arxiv.2409.19428},
   url           = {https://www.gerad.ca/fr/papers/G-2024-64},
 }
 
@@ -74,47 +73,47 @@ @TechReport{      diouane-gollier-orban-2024
   doi           = {10.13140/RG.2.2.16095.47527},
 }
 
-@Misc{orban-siqueira-cutest-2020,
-  author = {D. Orban and A. S. Siqueira and {contributors}},
-  title = {{CUTEst.jl}: {J}ulia's {CUTEst} interface},
-  month = {October},
-  url = {https://github.com/JuliaSmoothOptimizers/CUTEst.jl},
-  year = {2020},
-  DOI = {10.5281/zenodo.1188851},
+@Software{        orban-siqueira-cutest-2020,
+  author        = {D. Orban and A. S. Siqueira and {contributors}},
+  title         = {{CUTEst.jl}: {J}ulia's {CUTEst} interface},
+  month         = {October},
+  url           = {https://github.com/JuliaSmoothOptimizers/CUTEst.jl},
+  year          = {2020},
+  DOI           = {10.5281/zenodo.1188851},
 }
 
-@Misc{orban-siqueira-nlpmodels-2020,
-  author = {D. Orban and A. S. Siqueira and {contributors}},
-  title = {{NLPModels.jl}: Data Structures for Optimization Models},
-  month = {July},
-  url = {https://github.com/JuliaSmoothOptimizers/NLPModels.jl},
-  year = {2020},
-  DOI = {10.5281/zenodo.2558627},
+@Software{        orban-siqueira-nlpmodels-2020,
+  author        = {D. Orban and A. S. Siqueira and {contributors}},
+  title         = {{NLPModels.jl}: Data Structures for Optimization Models},
+  month         = {July},
+  url           = {https://github.com/JuliaSmoothOptimizers/NLPModels.jl},
+  year          = {2020},
+  DOI           = {10.5281/zenodo.2558627},
 }
 
-@Misc{jso,
-  author = {T. Migot and D. Orban and A. S. Siqueira},
-  title = {The {JuliaSmoothOptimizers} Ecosystem for Linear and Nonlinear Optimization},
-  year = {2021},
-  url = {https://juliasmoothoptimizers.github.io/},
-  doi = {10.5281/zenodo.2655082},
+@Software{        jso,
+  author        = {T. Migot and D. Orban and A. S. Siqueira},
+  title         = {The {JuliaSmoothOptimizers} Ecosystem for Linear and Nonlinear Optimization},
+  year          = {2021},
+  url           = {https://juliasmoothoptimizers.github.io/},
+  doi           = {10.5281/zenodo.2655082},
 }
 
-@Misc{migot-orban-siqueira-optimizationproblems-2023,
+@Software{       migot-orban-siqueira-optimizationproblems-2023,
   author       = {T. Migot and D. Orban and A. S. Siqueira},
-  title        = {OptimizationProblems.jl: A collection of optimization problems in Julia},
+  title        = {{OptimizationProblems.jl}: A collection of optimization problems in {J}ulia},
   year         = {2023},
   doi          = {10.5281/zenodo.3672094},
   url          = {https://github.com/JuliaSmoothOptimizers/OptimizationProblems.jl},
 }
 
-@techreport{kim-park-2008,
-  title = {Sparse Nonnegative Matrix Factorization for Clustering},
-  author = {Jingu Kim and Haesun Park},
-  institution = {Georgia Inst. of Technology},
-  number = {GT-CSE-08-01},
-  year = {2008},
-  url = {http://hdl.handle.net/1853/20058},
+@techreport{     kim-park-2008,
+  title        = {Sparse Nonnegative Matrix Factorization for Clustering},
+  author       = {Jingu Kim and Haesun Park},
+  institution  = {Georgia Inst. of Technology},
+  number       = {GT-CSE-08-01},
+  year         = {2008},
+  url          = {http://hdl.handle.net/1853/20058},
 }
 
 @InProceedings{   stella-themelis-sopasakis-patrinos-2017,
@@ -126,10 +125,10 @@ @InProceedings{   stella-themelis-sopasakis-patrinos-2017
   doi           = {10.1109/CDC.2017.8263933},
 }
 
-@article{demarchi-jia-kanzow-mehlitz-2023,
+@article{        demarchi-jia-kanzow-mehlitz-2023,
       author   = {De~Marchi, Alberto and Jia, Xiaoxi and Kanzow, Christian and Mehlitz, Patrick},
       title    = {Constrained composite optimization and augmented {L}agrangian methods},
-      journal  = {Mathematical Programming},
+      journal  = {Math. Program.},
       year     = {2023},
       month    = {9},
       volume   = {201},
@@ -140,22 +139,22 @@ @article{demarchi-jia-kanzow-mehlitz-2023
 
 @Article{         themelis-stella-patrinos-2017,
   Author        = {Themelis, Andreas and Stella, Lorenzo and Patrinos, Panagiotis},
-  Title         = {Forward-Backward Envelope for the Sum of Two Nonconvex Functions: Further Properties and Nonmonotone line seach Algorithms},
-  Journal       = siopt,
+  Title         = {Forward-Backward Envelope for the Sum of Two Nonconvex Functions: Further Properties and Nonmonotone line search Algorithms},
+  Journal       = {SIAM J. Optim.},
   Year          = 2018,
   Volume        = 28,
   Number        = 3,
   Pages         = {2274--2303},
   doi           = {10.1137/16M1080240},
 }
 
-@article{eckstein1992douglas,
-  title={On the Douglas—Rachford splitting method and the proximal point algorithm for maximal monotone operators},
-  author={Eckstein, Jonathan and Bertsekas, Dimitri P},
-  journal={Mathematical programming},
-  volume={55},
-  number={1},
-  pages={293--318},
-  year={1992},
-  publisher={Springer}
+@article{         eckstein-bertsekas-1992,
+  title         = {On the {D}ouglas—{R}achford splitting method and the proximal point algorithm for maximal monotone operators},
+  author        = {Eckstein, Jonathan and Bertsekas, Dimitri P},
+  journal       = {Math. Program.},
+  volume        = {55},
+  number        = {1},
+  pages         = {293--318},
+  year          = {1992},
+  publisher     = {Springer}
 }