Update to IMP 2.22.0, drop Python 2

Jupyter/spatiotemporal-colab.ipynb

@@ -181,7 +181,7 @@
     "\n",
     "Beads and Gaussians in our model belong to either a *rigid body* or *flexible string*. The positions of all beads and Gaussians in a single rigid body are constrained during sampling and do not move relative to each other. Meanwhile, flexible beads can move freely during sampling, but are restrained by sequence connectivity.\n",
     "\n",
-    "To begin, we built a topology file with the representation for the model of the complete system, `spatiotemporal_topology.txt`, located in `Heterogeneity/Heterogeneity_Modeling/`. This complete topology was used as a template to build topologies for each snapshot model. Based on our observation of the structure of the complex, we chose to represent each protein with at least 2 separate rigid bodies, and left the first 28 residues of protein C as flexible beads. Rigid bodies were described with 1 bead for every residue, and 10 residues per Gaussian. Flexible beads were described with 1 bead for every residue and 1 residue per Gaussian. A more complete description of the options available in topology files is available in the the [TopologyReader](https://integrativemodeling.org/2.21.0/doc/ref/classIMP_1_1pmi_1_1topology_1_1TopologyReader.html) documentation.\n",
+    "To begin, we built a topology file with the representation for the model of the complete system, `spatiotemporal_topology.txt`, located in `Heterogeneity/Heterogeneity_Modeling/`. This complete topology was used as a template to build topologies for each snapshot model. Based on our observation of the structure of the complex, we chose to represent each protein with at least 2 separate rigid bodies, and left the first 28 residues of protein C as flexible beads. Rigid bodies were described with 1 bead for every residue, and 10 residues per Gaussian. Flexible beads were described with 1 bead for every residue and 1 residue per Gaussian. A more complete description of the options available in topology files is available in the the [TopologyReader](https://integrativemodeling.org/2.22.0/doc/ref/classIMP_1_1pmi_1_1topology_1_1TopologyReader.html) documentation.\n",
     "\n",
     "```\n",
     "|molecule_name | color | fasta_fn | fasta_id | pdb_fn | chain | residue_range | pdb_offset | bead_size | em_residues_per_gaussian | rigid_body | super_rigid_body | chain_of_super_rigid_bodies | \n",
@@ -1286,7 +1286,7 @@
    "source": [
     "# Next steps<a id=\"notebook_Conclusion\"></a>\n",
     "\n",
-    "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.21.0/doc/manual/intro.html#procedure).\n",
+    "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.22.0/doc/manual/intro.html#procedure).\n",
     "\n",
     "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-IHM database](https://pdb-ihm.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
    ]

Jupyter/spatiotemporal.ipynb

@@ -156,7 +156,7 @@
     "\n",
     "Beads and Gaussians in our model belong to either a *rigid body* or *flexible string*. The positions of all beads and Gaussians in a single rigid body are constrained during sampling and do not move relative to each other. Meanwhile, flexible beads can move freely during sampling, but are restrained by sequence connectivity.\n",
     "\n",
-    "To begin, we built a topology file with the representation for the model of the complete system, `spatiotemporal_topology.txt`, located in `Heterogeneity/Heterogeneity_Modeling/`. This complete topology was used as a template to build topologies for each snapshot model. Based on our observation of the structure of the complex, we chose to represent each protein with at least 2 separate rigid bodies, and left the first 28 residues of protein C as flexible beads. Rigid bodies were described with 1 bead for every residue, and 10 residues per Gaussian. Flexible beads were described with 1 bead for every residue and 1 residue per Gaussian. A more complete description of the options available in topology files is available in the the [TopologyReader](https://integrativemodeling.org/2.21.0/doc/ref/classIMP_1_1pmi_1_1topology_1_1TopologyReader.html) documentation.\n",
+    "To begin, we built a topology file with the representation for the model of the complete system, `spatiotemporal_topology.txt`, located in `Heterogeneity/Heterogeneity_Modeling/`. This complete topology was used as a template to build topologies for each snapshot model. Based on our observation of the structure of the complex, we chose to represent each protein with at least 2 separate rigid bodies, and left the first 28 residues of protein C as flexible beads. Rigid bodies were described with 1 bead for every residue, and 10 residues per Gaussian. Flexible beads were described with 1 bead for every residue and 1 residue per Gaussian. A more complete description of the options available in topology files is available in the the [TopologyReader](https://integrativemodeling.org/2.22.0/doc/ref/classIMP_1_1pmi_1_1topology_1_1TopologyReader.html) documentation.\n",
     "\n",
     "```\n",
     "|molecule_name | color | fasta_fn | fasta_id | pdb_fn | chain | residue_range | pdb_offset | bead_size | em_residues_per_gaussian | rigid_body | super_rigid_body | chain_of_super_rigid_bodies | \n",
@@ -1261,7 +1261,7 @@
    "source": [
     "# Next steps<a id=\"notebook_Conclusion\"></a>\n",
     "\n",
-    "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.21.0/doc/manual/intro.html#procedure).\n",
+    "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.22.0/doc/manual/intro.html#procedure).\n",
     "\n",
     "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-IHM database](https://pdb-ihm.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
    ]

support/setup_ci.sh

@@ -20,20 +20,8 @@ else
   IMP_CONDA="imp"
 fi
 
-if [ ${python_version} = "2.7" ]; then
-  pip="pip<=19.3.1"
-else
-  pip="pip"
-fi
-
-conda create --yes -q -n python${python_version} -c salilab python=${python_version} scipy matplotlib pandas scikit-learn ${pip} ${IMP_CONDA}
+conda create --yes -q -n python${python_version} -c salilab python=${python_version} scipy matplotlib pandas scikit-learn pip ${IMP_CONDA}
 eval "$(conda shell.bash hook)"
 conda activate python${python_version}
 
-if [ ${python_version} = "2.7" ]; then
-  # pytest-flake8 1.1.0 tries to import contextlib.redirect_stdout, which
-  # isn't present in Python 2
-  pip install pytest-cov coverage 'pytest-flake8<1.1'
-else
-  pip install pytest-cov coverage pytest-flake8
-fi
+pip install pytest-cov coverage pytest-flake8