Dev (#102)

* Updating causal-cmd Dockerfile 1.11.1 * Updating trilearn to fix but in trilearn_pgibbs.
felixleopoldo · Nov 30, 2023 · 3754a47 · 3754a47
1 parent 395bcdd
commit 3754a47
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Showing 21 changed files with 87 additions and 44 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.6.0
+2.6.1
diff --git a/config/chordal_algos.json b/config/chordal_algos.json
@@ -3,11 +3,11 @@
         "data": [
             {
                 "data_id": "example1",
-                "graph_id": "cta",
+                "graph_id": "AR1-5",
                 "parameters_id": "intra-class",
                 "seed_range": [
                     1,
-                    5
+                    1
                 ]
             }
         ],
@@ -21,7 +21,7 @@
                 "path": true,
                 "text": false,
                 "ids": [
-                    "gg99"
+                    "gg99", "trilearn"
                 ]
             },
             "graph_true_plots": true,
@@ -33,27 +33,43 @@
             "mcmc_traj_plots": [
                 {
                     "id": "gg99",
-                    "burn_in": 0,
-                    "thinning": 10,
+                    "burn_in": 0.5,
+                    "thinning": 1000,
+                    "functional": [
+                        "score",
+                        "size"
+                    ],
+                    "active": true
+                },
+                {
+                    "id": "trilearn",
+                    "burn_in": 0.5,
+                    "thinning": 1,
                     "functional": [
                         "score",
                         "size"
                     ],
                     "active": true
                 }
+
             ],
             "mcmc_heatmaps": [
                 {
                     "id": "gg99",
                     "burn_in": 0.5,
                     "active": true
+                },
+                {
+                    "id": "trilearn",
+                    "burn_in": 0.5,
+                    "active": true
                 }
             ],
             "mcmc_autocorr_plots": [
                 {
                     "id": "gg99",
                     "burn_in": 0.5,
-                    "thinning": 100,
+                    "thinning": 1000,
                     "lags": 50,
                     "functional": [
                         "score",
@@ -81,13 +97,13 @@
                 {
                     "id": "AR1-5",
                     "max_bandwidth": 5,
-                    "dim": 10000
+                    "dim": 50
                 }
             ],
             "trilearn_cta": [
                 {
                     "id": "cta",
-                    "order": 100,
+                    "order": 50,
                     "alpha": 0.5,
                     "beta": 0.5
                 }
@@ -114,12 +130,18 @@
                 {
                     "id": "gg99",
                     "burnin_frac": 0.5,
-                    "mcmc_estimator": "map",
+                    "mcmc_estimator": "threshold",
                     "timeout": null,
-                    "threshold": 0.5,
-                    "mcmc_seed": [1, 2, 3],
+                    "threshold": [0.2, 0.5, 0.9],
+                    "mcmc_seed": [
+                        1,
+                        2,
+                        3
+                    ],
                     "num_samples": 1000000,
-                    "sampler": [0, 1],
+                    "sampler": [
+                        1
+                    ],
                     "edge_penalty": 1.0,
                     "size_maxclique": 10000
                 }
@@ -147,6 +169,27 @@
                     "mcmc_estimator": "map",
                     "timeout": null
                 }
+            ],
+            "trilearn_pgibbs": [
+                {
+                    "id": "trilearn",
+                    "datatype": "continuous",
+                    "alpha": 0.5,
+                    "beta": 0.5,
+                    "radii": 80,
+                    "n_particles": 20,
+                    "M": 2000,
+                    "pseudo_obs": 1,
+                    "mcmc_seed": [1,2,3],
+                    "mcmc_estimator": "threshold",
+                    "threshold": [
+                        0.2,
+                        0.5,
+                        0.9
+                    ],
+                    "burnin_frac": 0.5,
+                    "timeout": null
+                }
             ]
         }
     }

diff --git a/docs/source/available_graphs.rst b/docs/source/available_graphs.rst
@@ -40,17 +40,17 @@ Below is a list of available modules.
    * - Band matrix
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
-     - 1.25
+     - 2.0.4
      - trilearn_bandmat_ 
    * - CTA
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
-     - 1.25
+     - 2.0.4
      - trilearn_cta_ 
    * - Random bandmatrix
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
-     - 1.25
+     - 2.0.4
      - trilearn_rand_bandmat_ 
 
 
@@ -206,7 +206,7 @@ trilearn_bandmat
    * - Package
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
    * - Version
-     - 1.25
+     - 2.0.4
    * - Language
      - `Python <https://www.python.org/>`__
    * - Docs
@@ -216,7 +216,7 @@ trilearn_bandmat
    * - Graph type
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
    * - Docker 
-     - `bpimages/trilearn:2.0.3 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
+     - `bpimages/trilearn:2.0.4.0 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
 
    * - Module
      - `trilearn_bandmat <https://github.com/felixleopoldo/benchpress/tree/master/workflow/rules/graph/trilearn_bandmat>`__
@@ -260,7 +260,7 @@ trilearn_cta
    * - Package
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
    * - Version
-     - 1.25
+     - 2.0.4
    * - Language
      - `Python <https://www.python.org/>`__
    * - Docs
@@ -270,7 +270,7 @@ trilearn_cta
    * - Graph type
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
    * - Docker 
-     - `bpimages/trilearn:2.0.3 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
+     - `bpimages/trilearn:2.0.4.0 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
 
    * - Module
      - `trilearn_cta <https://github.com/felixleopoldo/benchpress/tree/master/workflow/rules/graph/trilearn_cta>`__
@@ -319,7 +319,7 @@ trilearn_rand_bandmat
    * - Package
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
    * - Version
-     - 1.25
+     - 2.0.4
    * - Language
      - `Python <https://www.python.org/>`__
    * - Docs
@@ -329,7 +329,7 @@ trilearn_rand_bandmat
    * - Graph type
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
    * - Docker 
-     - `bpimages/trilearn:2.0.3 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
+     - `bpimages/trilearn:2.0.4.0 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
 
    * - Module
      - `trilearn_rand_bandmat <https://github.com/felixleopoldo/benchpress/tree/master/workflow/rules/graph/trilearn_rand_bandmat>`__

diff --git a/docs/source/available_parameters.rst b/docs/source/available_parameters.rst
@@ -289,7 +289,7 @@ trilearn_hyper-dir
    * - Graph type
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
    * - Docker 
-     - `bpimages/trilearn:2.0.3 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
+     - `bpimages/trilearn:2.0.4.0 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
    * - Module
      - `trilearn_hyper-dir <https://github.com/felixleopoldo/benchpress/tree/master/workflow/rules/parameters/trilearn_hyper-dir>`__
 
@@ -345,7 +345,7 @@ trilearn_intra-class
    * - Graph type
      - `UG <https://en.wikipedia.org/wiki/Graph_(discrete_mathematics)#Graph>`__
    * - Docker 
-     - `bpimages/trilearn:2.0.3 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
+     - `bpimages/trilearn:2.0.4.0 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
    * - Module
      - `trilearn_intra-class <https://github.com/felixleopoldo/benchpress/tree/master/workflow/rules/parameters/trilearn_intra-class>`__
 

diff --git a/docs/source/available_structure_learning_algorithms.rst b/docs/source/available_structure_learning_algorithms.rst
@@ -4213,7 +4213,7 @@ trilearn_pgibbs
    * - Package
      - `trilearn <https://github.com/felixleopoldo/trilearn>`__
    * - Version
-     - 1.25
+     - 2.0.4
    * - Language
      - `Python <https://www.python.org/>`__
    * - Docs
@@ -4223,7 +4223,7 @@ trilearn_pgibbs
    * - Graph type
      - `DG <https://en.wikipedia.org/wiki/Chordal_graph>`__
    * - Docker 
-     - `bpimages/trilearn:2.0.3 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
+     - `bpimages/trilearn:2.0.4.0 <https://hub.docker.com/r/bpimages/trilearn/tags>`__
 
    * - Module folder
      - `trilearn_pgibbs <https://github.com/felixleopoldo/benchpress/tree/master/workflow/rules/structure_learning_algorithms/trilearn_pgibbs>`__

diff --git a/workflow/envs/Dockerfile.causal-cmd b/workflow/envs/Dockerfile.causal-cmd
@@ -3,7 +3,7 @@ FROM r-base:4.1.0
 RUN apt update -y
 RUN apt install -y default-jre
 WORKDIR /tetrad
-RUN wget https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/causal-cmd/1.11.0/causal-cmd-1.11.0-jar-with-dependencies.jar
+RUN wget https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/causal-cmd/1.11.1/causal-cmd-1.11.1-jar-with-dependencies.jar
 RUN apt install time
 
 RUN R -e 'install.packages("remotes")' 

diff --git a/workflow/envs/Dockerfile.trilearn b/workflow/envs/Dockerfile.trilearn
@@ -3,4 +3,4 @@ FROM python:3.11.5
 RUN apt update -y
 RUN apt install -y graphviz libgraphviz-dev
 RUN apt install time 
-RUN pip install trilearn==2.0.3
+RUN pip install trilearn==2.0.4
diff --git a/workflow/envs/build_images.sh b/workflow/envs/build_images.sh
@@ -24,17 +24,17 @@ declare -A image_versions
 # image_versions[pcalg]=2.7-8
 # image_versions[bnlearn]=4.8.3
 # image_versions[bidag]=2.1.4
-# image_versions[causal-cmd]=1.11.0
+# image_versions[causal-cmd]=1.11.1
 # image_versions[equsa_psilearner]=1.2.1
 # image_versions[benchpress]=2.1.0
 # image_versions[causaldag]=0.1a163
 # image_versions[gcastle]=1.0.3
 # image_versions[sandbox]=1.0
 # image_versions[datascience-python]=1.1
-# image_versions[trilearn]=2.0.3
+image_versions[trilearn]=2.0.4.0
 # image_versions[snakemake]=v7.32.3
 # image_versions[gobnilp]=4347c64
-image_versions[grues]=0.3.0
+# image_versions[grues]=0.3.0
 
 # Build the image for amd64 and arm64 and push them to dockerhub and create the manifest and push it
 # Run this twice or so as some packages depend on rgraphstuff and pcalg e.g.

diff --git a/workflow/rules/docker_images.smk b/workflow/rules/docker_images.smk
@@ -2,7 +2,7 @@
 
 def docker_image(name):
     if name == "trilearn":
-        return "docker://bpimages/trilearn:2.0.3"
+        return "docker://bpimages/trilearn:2.0.4.0"
     elif name == "pydatascience":
         return "docker://bpimages/datascience-python:1.1"
     elif name == "bidag":

diff --git a/workflow/rules/graph/trilearn_bandmat/info.json b/workflow/rules/graph/trilearn_bandmat/info.json
@@ -1,6 +1,6 @@
 {
     "title": "Band matrix",
-    "version": "1.25",
+    "version": "2.0.4",
     "package": {
         "title": "trilearn",
         "url": "https://github.com/felixleopoldo/trilearn"

diff --git a/workflow/rules/graph/trilearn_bandmat/rule.smk b/workflow/rules/graph/trilearn_bandmat/rule.smk
@@ -2,6 +2,6 @@ rule trilearn_bandmat:
     output:
         adjmat = "{output_dir}/adjmat/" + pattern_strings["trilearn_bandmat"] + "/seed={seed}.csv"
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         "python workflow/rules/graph/trilearn_bandmat/trilearn_gen_bandmat.py {output.adjmat} {wildcards.seed} {wildcards.dim} {wildcards.bandwidth}"
diff --git a/workflow/rules/graph/trilearn_cta/info.json b/workflow/rules/graph/trilearn_cta/info.json
@@ -1,6 +1,6 @@
 {
     "title": "CTA",
-    "version": "1.25",
+    "version": "2.0.4",
     "package": {
         "title": "trilearn",
         "url": "https://github.com/felixleopoldo/trilearn"

diff --git a/workflow/rules/graph/trilearn_cta/rule.smk b/workflow/rules/graph/trilearn_cta/rule.smk
@@ -2,6 +2,6 @@ rule sample_adjmat_cta:
     output:
         adjmat = "{output_dir}/adjmat/" + pattern_strings["trilearn_cta"] + "/seed={seed}.csv"
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         "python workflow/rules/graph/trilearn_cta/trilearn_sample_cta.py {output.adjmat} {wildcards.seed} {wildcards.order} {wildcards.alpha} {wildcards.beta} "
diff --git a/workflow/rules/graph/trilearn_rand_bandmat/info.json b/workflow/rules/graph/trilearn_rand_bandmat/info.json
@@ -1,6 +1,6 @@
 {
     "title": "Random bandmatrix",
-    "version": "1.25",
+    "version": "2.0.4",
     "package": {
         "title": "trilearn",
         "url": "https://github.com/felixleopoldo/trilearn"

diff --git a/workflow/rules/graph/trilearn_rand_bandmat/rule.smk b/workflow/rules/graph/trilearn_rand_bandmat/rule.smk
@@ -3,6 +3,6 @@ rule trilearn_rand_bandmat:
     output:
         adjmat = "{output_dir}/adjmat/" + pattern_strings["trilearn_rand_bandmat"] + "/seed={seed}.csv"
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         "python workflow/rules/graph/trilearn_rand_bandmat/trilearn_rand_bandmat.py {output.adjmat} {wildcards.seed} {wildcards.dim} {wildcards.max_bandwidth}"
diff --git a/workflow/rules/graph/trilearn_rand_bandmat/trilearn_rand_bandmat.py b/workflow/rules/graph/trilearn_rand_bandmat/trilearn_rand_bandmat.py
@@ -15,6 +15,6 @@
 np.random.seed(seed)
 g = dlib.sample_random_AR_graph(dim, max_bandwidth)
 
-m = nx.to_numpy_matrix(g)
+m = nx.to_numpy_array(g)
 df = pd.DataFrame(m, dtype=int)
 df.to_csv(filename, index=None)
diff --git a/workflow/rules/parameters/trilearn_g_inv_wishart/rule.smk b/workflow/rules/parameters/trilearn_g_inv_wishart/rule.smk
@@ -8,6 +8,6 @@ rule trilearn_g_inv_wishart:
                 "seed={seed}/"+\
                 "adjmat=/{adjmat}.csv"
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         "python workflow/rules/parameters/trilearn_g_in_wishart/trilearn_g_inv_wishart_cov.py {input.adjmat} {output.params} {wildcards.dof} {wildcards.seed}"
diff --git a/workflow/rules/parameters/trilearn_hyper-dir/rule.smk b/workflow/rules/parameters/trilearn_hyper-dir/rule.smk
@@ -8,6 +8,6 @@ rule trilearn_hyper_dir:
                 "seed={seed}/"+\
                 "adjmat=/{adjmat}.json"
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         "python workflow/rules/parameters/trilearn_hyper-dir/trilearn_sample_hyper-dir.py {output.bn} {wildcards.seed} {wildcards.n_levels} {wildcards.pseudo_obs} {input.adjmat}" 
diff --git a/workflow/rules/parameters/trilearn_intra-class/rule.smk b/workflow/rules/parameters/trilearn_intra-class/rule.smk
@@ -8,6 +8,6 @@ rule intra_class_cov:
                 "seed={seed}/"+\
                 "adjmat=/{adjmat}.csv"
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         "python workflow/rules/parameters/trilearn_intra-class/trilearn_g_intra_class_cov.py {input.adjmat} {output.params} {wildcards.rho} {wildcards.sigma2}"
diff --git a/workflow/rules/structure_learning_algorithms/trilearn_pgibbs/info.json b/workflow/rules/structure_learning_algorithms/trilearn_pgibbs/info.json
@@ -1,6 +1,6 @@
 {
     "title": "Particle Gibbs",
-    "version": "1.25",
+    "version": "2.0.4",
     "package": {
         "title": "trilearn",
         "url": "https://github.com/felixleopoldo/trilearn"

diff --git a/workflow/rules/structure_learning_algorithms/trilearn_pgibbs/rule.smk b/workflow/rules/structure_learning_algorithms/trilearn_pgibbs/rule.smk
@@ -9,7 +9,7 @@ rule:
         time=alg_output_time_path(module_name),
         ntests=touch(alg_output_ntests_path(module_name))
     container:
-        "docker://bpimages/trilearn:2.0.3"
+        "docker://bpimages/trilearn:2.0.4.0"
     shell:
         """
         if [ {wildcards.timeout} = \"None\" ]; then