biopipen 0.30.0__tar.gz → 0.31.1__tar.gz

{biopipen-0.30.0 → biopipen-0.31.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.30.0
+Version: 0.31.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -14,9 +14,9 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: runinfo
 Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
-Requires-Dist: pipen-board[report] (>=0.15,<0.16)
-Requires-Dist: pipen-cli-run (>=0.13,<0.14)
-Requires-Dist: pipen-filters (>=0.13,<0.14)
-Requires-Dist: pipen-poplog (>=0.1.2,<0.2.0)
-Requires-Dist: pipen-runinfo (>=0.6,<0.7) ; extra == "runinfo"
-Requires-Dist: pipen-verbose (>=0.11,<0.12)
+Requires-Dist: pipen-board[report] (>=0.16,<0.17)
+Requires-Dist: pipen-cli-run (>=0.14,<0.15)
+Requires-Dist: pipen-filters (>=0.14,<0.15)
+Requires-Dist: pipen-poplog (>=0.2.0,<0.3.0)
+Requires-Dist: pipen-runinfo (>=0.7,<0.8) ; extra == "runinfo"
+Requires-Dist: pipen-verbose (>=0.12,<0.13)

biopipen-0.31.1/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.31.1"

{biopipen-0.30.0 → biopipen-0.31.1}/biopipen/ns/scrna.py

@@ -541,14 +541,19 @@ class SeuratClusterStats(Proc):
             This is to do some basic statistics on the clusters. For more comprehensive analysis,
             see `RadarPlots` and `CellsDistribution`.
             The parameters from the cases can overwrite the default parameters.
-            - frac (flag): Whether to output the fraction of cells instead of number.
+            - frac (choice): How to calculate the fraction of cells.
+                - group: calculate the fraction in each group.
+                    The total fraction of the cells of idents in each group will be 1.
+                    When `group-by` is not specified, it will be the same as `all`.
+                - ident: calculate the fraction in each ident.
+                    The total fraction of the cells of groups in each ident will be 1.
+                    Only works when `group-by` is specified.
+                - cluster: alias of `ident`.
+                - all: calculate the fraction against all cells.
+                - none: do not calculate the fraction, use the number of cells instead.
             - pie (flag): Also output a pie chart?
             - circos (flag): Also output a circos plot?
             - table (flag): Whether to output a table (in tab-delimited format) and in the report.
-            - frac_ofall (flag): Whether to output the fraction against all cells,
-                instead of the fraction in each group.
-                Does not work for circos plot.
-                Only works when `frac` is `True` and `group-by` is specified.
             - transpose (flag): Whether to transpose the cluster and group, that is,
                 using group as the x-axis and cluster to fill the plot.
                 For circos plot, when transposed, the arrows will be drawn from the idents (by `ident`) to the
@@ -708,12 +713,11 @@ class SeuratClusterStats(Proc):
         },
         "hists": {},
         "stats_defaults": {
-            "frac": False,
+            "frac": "none",
             "pie": False,
             "circos": False,
             "table": False,
             "position": "auto",
-            "frac_ofall": False,
             "transpose": False,
             "ident": "seurat_clusters",
             "group-by": None,
@@ -731,7 +735,7 @@ class SeuratClusterStats(Proc):
             "Number of cells in each cluster by Sample": {
                 "group-by": "Sample",
                 "table": True,
-                "frac": True,
+                "frac": "group",
             },
         },
         "ngenes_defaults": {
@@ -2261,3 +2265,52 @@ class AnnData2Seurat(Proc):
     lang = config.lang.rscript
     envs = {"outtype": "rds", "assay": "RNA", "dotplot_check": True}
     script = "file://../scripts/scrna/AnnData2Seurat.R"
+
+
+class ScSimulation(Proc):
+    """Simulate single-cell data using splatter.
+
+    See <https://www.bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html#2_Quickstart>
+
+    Input:
+        seed: The seed for the simulation
+            You could also use string as the seed, and the seed will be
+            generated by `digest::digest2int()`.
+            So this could also work as a unique identifier for the simulation (ie. Sample ID).
+
+    Output:
+        outfile: The output Seurat object/SingleCellExperiment in RDS format
+
+    Envs:
+        ngenes (type=int): The number of genes to simulate
+        ncells (type=int): The number of cells to simulate
+        nspikes (type=int): The number of spike-ins to simulate
+            When `ngenes`, `ncells`, and `nspikes` are not specified, the default
+            params from `mockSCE()` will be used. By default, `ngenes = 2000`,
+            `ncells = 200`, and `nspikes = 100`.
+        outtype (choice): The output file type.
+            - seurat: Seurat object
+            - singlecellexperiment: SingleCellExperiment object
+            - sce: alias for `singlecellexperiment`
+        method (choice): which simulation method to use. Options are:
+            - single: produces a single population
+            - groups: produces distinct groups (eg. cell types), or
+            - paths: selects cells from continuous trajectories (eg. differentiation processes)
+        params (ns): Other parameters for simulation.
+            The parameters are initialized `splitEstimate(mockSCE())` and then
+            updated with the given parameters.
+            See <https://rdrr.io/bioc/splatter/man/SplatParams.html>.
+            Hyphens (`-`) will be transformed into dots (`.`) for the keys.
+    """  # noqa: E501
+    input = "seed:var"
+    output = "outfile:file:simulatied_{{in.seed}}.RDS"
+    lang = config.lang.rscript
+    envs = {
+        "ngenes": None,
+        "ncells": None,
+        "nspikes": None,
+        "outtype": "seurat",
+        "method": "single",
+        "params": {},
+    }
+    script = "file://../scripts/scrna/ScSimulation.R"

{biopipen-0.30.0 → biopipen-0.31.1}/biopipen/scripts/scrna/CellsDistribution.R

@@ -325,7 +325,7 @@ do_case <- function(name, case) {
             geom_col(width=.01, position="fill", color = "#888888") +
             geom_bar(stat = "identity", position = position_fill(reverse = TRUE)) +
             coord_polar("y", start = 0) +
-            scale_fill_biopipen(name = "Cluster", limits = levels(all_clusters)) +
+            scale_fill_manual(name = "Cluster", values = pal_biopipen()(length(levels(all_clusters)))) +
             theme_void() +
             theme(
                 plot.margin = plot.margin,

biopipen-0.31.1/biopipen/scripts/scrna/ScSimulation.R

@@ -0,0 +1,64 @@
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+
+library(rlang)
+library(splatter)
+library(scater)
+
+# Load template variables
+seed <- {{ in.seed | r }}
+outfile <- {{ out.outfile | r }}
+ngenes <- {{ envs.ngenes | r }}
+ncells <- {{ envs.ncells | r }}
+nspikes <- {{ envs.nspikes | r }}
+outtype <- {{ envs.outtype | r }}
+method <- {{ envs.method | r }}
+user_params <- {{ envs.params | r: todot="-" }}
+
+log_info("Generating simulation parameters ...")
+
+seed <- seed %||% 1
+if (length(seed) > 1) {
+    log_warn("- multiple seeds provided, using the first one")
+    seed <- seed[1]
+}
+if (is.character(seed)) {
+    library(digest)
+    proj <- seed
+    seed <- digest2int(seed)
+} else {
+    proj <- paste0("S", seed)
+}
+
+set.seed(seed)
+mock_sce_params <- list()
+if (!is.null(ngenes)) mock_sce_params$ngenes <- ngenes
+if (!is.null(ncells)) mock_sce_params$ncells <- ncells
+if (!is.null(nspikes)) mock_sce_params$nspikes <- nspikes
+sce <- do.call(mockSCE, mock_sce_params)
+params <- splatEstimate(sce)
+user_params$seed <- seed
+user_params$object = params
+do_call(setParams, user_params)
+
+
+log_info("Saving simulation parameters to file ...")
+
+sim <- splatSimulate(params, method = method, verbose = TRUE)
+
+outtype <- tolower(outtype)
+if (outtype == "sce") outtype <- "singlecellexperiment"
+
+if (outtype == "singlecellexperiment") {
+    log_info("Saving simulation to file ...")
+    saveRDS(sim, file = outfile)
+} else {
+    log_info("Converting simulation to Seurat object ...")
+    cnts <- SingleCellExperiment::counts(sim)
+    sobj <- Seurat::CreateSeuratObject(counts = cnts, project = proj)
+    rm(sim)
+    rm(cnts)
+    gc()
+
+    log_info("Saving simulation to file ...")
+    saveRDS(sobj, file = outfile)
+}

{biopipen-0.30.0 → biopipen-0.31.1}/biopipen/scripts/scrna/SeuratClusterStats-stats.R

@@ -18,12 +18,6 @@ do_one_stats = function(name) {
     if (isTRUE(case$pie) && !is.null(case$group.by)) {
         stop(paste0(name, ": pie charts are not supported for group-by"))
     }
-    if (!isTRUE(case$frac) && isTRUE(case$frac_ofall)) {
-        stop(paste0(name, ": frac_ofall is only supported when frac is true"))
-    }
-    if (isTRUE(case$frac_ofall) && is.null(case$group.by)) {
-        stop(paste0(name, ": frac_ofall is only supported for group-by"))
-    }
     if (isTRUE(case$transpose) && is.null(case$group.by)) {
         stop(paste0(name, ": transpose is only supported for group-by"))
     }
@@ -46,28 +40,28 @@ do_one_stats = function(name) {
             !!!syms(case$split.by)
         ), function(df) {
             out <- df %>% group_by(!!!syms(select_cols)) %>% summarise(.n = n(), .groups = "drop")
-            if (!is.null(case$group.by) && isTRUE(case$frac)) {
-                if (isTRUE(case$frac_ofall)) {
+            if (!is.null(case$group.by) && case$frac != "none") {
+                if (case$frac == "all") {
                     out <- out %>% mutate(.frac = .n / sum(.n))
-                } else if (isTRUE(case$transpose)) {
-                    out <- out %>% group_by(!!sym(case$ident)) %>% mutate(.frac = .n / sum(.n))
-                } else {
+                } else if (case$frac == "group") {
                     out <- out %>% group_by(!!sym(case$group.by)) %>% mutate(.frac = .n / sum(.n))
+                } else {  # case$frac == "ident" or "cluster"
+                    out <- out %>% group_by(!!sym(case$ident)) %>% mutate(.frac = .n / sum(.n))
                 }
             }
             out
         }))
-    } else if (!is.null(case$group.by) && isTRUE(case$frac)) {
+    } else if (!is.null(case$group.by) && case$frac != "none") {  # no split.by
         plot_df <- df_cells %>%
             select(all_of(select_cols)) %>%
             group_by(!!!syms(select_cols)) %>%
             summarise(.n = n(), .groups = "drop")
-        if (isTRUE(case$frac_ofall)) {
+        if (case$frac == "all") {
             plot_df = plot_df %>% mutate(.frac = .n / sum(.n))
-        } else {
-            plot_df = plot_df %>%
-                group_by(!!sym(ifelse(isTRUE(case$transpose), case$group.by, case$ident))) %>%
-                mutate(.frac = .n / sum(.n))
+        } else if (case$frac == "group") {
+            plot_df = plot_df %>% group_by(!!sym(case$group.by)) %>% mutate(.frac = .n / sum(.n))
+        } else {  # case$frac == "ident" or "cluster"
+            plot_df = plot_df %>% group_by(!!sym(case$ident)) %>% mutate(.frac = .n / sum(.n))
         }
     } else {
         plot_df <- df_cells %>%
@@ -75,7 +69,7 @@ do_one_stats = function(name) {
             group_by(!!!syms(select_cols)) %>%
             summarise(.n = n(), .groups = "drop")
 
-        if (isTRUE(case$frac) || isTRUE(case$frac_ofall)) {
+        if (case$frac != "none") {
             plot_df <- plot_df %>% mutate(.frac = .n / sum(.n))
         }
     }
@@ -88,13 +82,13 @@ do_one_stats = function(name) {
     p = plot_df %>%
         ggplot(aes(
             x=!!sym(ifelse(case$transpose, case$group.by, case$ident)),
-            y=if (isTRUE(case$frac)) .frac else .n,
+            y=if (case$frac != "none") .frac else .n,
             fill=!!sym(ifelse(is.null(case$group.by) || isTRUE(case$transpose), case$ident, case$group.by))
         )) +
         geom_bar(stat="identity", position=bar_position, alpha=.8) +
         theme_prism(axis_text_angle = 90) +
         scale_fill_biopipen() +
-        ylab(ifelse(isTRUE(case$frac), "Fraction of cells", "Number of cells"))
+        ylab(ifelse(case$frac != "none", "Fraction of cells", "Number of cells"))
 
     if (!is.null(case$split.by)) {
         p = p + facet_wrap(case$split.by)
@@ -109,7 +103,7 @@ do_one_stats = function(name) {
             kind = "descr",
             content = paste0(
                 "Plots showing the ",
-                ifelse(isTRUE(case$frac), "number/faction", "number"),
+                ifelse(case$frac != "none", "number/faction", "number"),
                 " of cells per cluster",
                 ifelse(
                     is.null(case$group.by),
@@ -150,7 +144,7 @@ do_one_stats = function(name) {
             guides(fill = guide_legend(title = case$ident)) +
             theme_void() +
             geom_label(
-                if (isTRUE(case$frac))
+                if (case$frac != "none")
                     aes(label=sprintf("%.1f%%", .frac * 100))
                 else
                     aes(label=.n),

{biopipen-0.30.0 → biopipen-0.31.1}/biopipen/scripts/scrna/SeuratMap2Ref.R

@@ -45,6 +45,10 @@ if (is.null(split_by)) {
     future::plan(strategy = "multicore", workers = ncores)
 }
 
+.is_sct <- function(x) {
+    return(Seurat:::IsSCT(assay = x@assays[[DefaultAssay(x)]]))
+}
+
 .expand_dims = function(args, name = "dims") {
     # Expand dims from 30 to 1:30
     if (is.numeric(args[[name]]) && length(args[[name]] == 1)) {
@@ -63,6 +67,8 @@ if (endsWith(ref, ".rds") || endsWith(ref, ".RDS")) {
 } else {
     reference = LoadH5Seurat(ref)
 }
+reference = UpdateSeuratObject(reference)
+reference = UpdateSCTAssays(reference)
 
 # check if refdata exists in the reference
 for (rname in names(mapquery_args$refdata)) {
@@ -84,9 +90,20 @@ for (rname in names(mapquery_args$refdata)) {
     }
 }
 
-if (refnorm == "auto" && DefaultAssay(reference) == "SCT") {
+if (refnorm == "auto" && .is_sct(reference)) {
     refnorm = "SCTransform"
 }
+if (refnorm == "SCTransform") {
+    # Check if the reference is SCTransform'ed
+    if (!.is_sct(reference)) {
+        stop("Reference is not SCTransform'ed")
+    }
+    n_models = length(x = slot(object = reference[[DefaultAssay(reference)]], name = "SCTModel.list"))
+    if (n_models == 0) {
+        stop("Reference doesn't contain SCTModel.")
+    }
+}
+
 log_info("  Normalization method used: {refnorm}")
 if (refnorm == "SCTransform") {
     findtransferanchors_args$normalization.method = "SCT"
@@ -130,18 +147,17 @@ log_info("- Normalizing data")
 if (refnorm == "SCTransform") {
     if (defassay == "SCT" && skip_if_normalized) {
         log_warn("  Skipping normalization as the object is already SCTransform'ed")
-        query = sobj
     } else {
         log_info("  Using SCTransform normalization")
         sctransform_args$residual.features = rownames(x = reference)
         if (is.null(split_by)) {
             sctransform_args$object = sobj
-            query = do_call(SCTransform, sctransform_args)
+            sobj = do_call(SCTransform, sctransform_args)
             sctransform_args$object <- NULL
             rm(sctransform_args)
             gc()
         } else {
-            query = mclapply(
+            sobj = mclapply(
                 X = sobj,
                 FUN = function(x) {
                     sctransform_args$object = x
@@ -149,22 +165,21 @@ if (refnorm == "SCTransform") {
                 },
                 mc.cores = ncores
             )
-            if (any(unlist(lapply(query, class)) == "try-error")) {
-                stop(paste0("\nmclapply (SCTransform) error:", query))
+            if (any(unlist(lapply(sobj, class)) == "try-error")) {
+                stop(paste0("\nmclapply (SCTransform) error:", sobj))
             }
         }
     }
 } else {
     if (defassay == "RNA" && skip_if_normalized) {
         log_warn("  Skipping normalization as the object is already LogNormalize'd")
-        query = sobj
     } else {
         log_info("  Using NormalizeData normalization")
         if (is.null(split_by)) {
             normalizedata_args$object = sobj
-            query = do_call(NormalizeData, normalizedata_args)
+            sobj = do_call(NormalizeData, normalizedata_args)
         } else {
-            query = mclapply(
+            sobj = mclapply(
                 X = sobj,
                 FUN = function(x) {
                     normalizedata_args$object = x
@@ -172,8 +187,8 @@ if (refnorm == "SCTransform") {
                 },
                 mc.cores = ncores
             )
-            if (any(unlist(lapply(query, class)) == "try-error")) {
-                stop(paste0("\nmclapply (NormalizeData) error:", query))
+            if (any(unlist(lapply(sobj, class)) == "try-error")) {
+                stop(paste0("\nmclapply (NormalizeData) error:", sobj))
             }
         }
         normalizedata_args$object <- NULL
@@ -181,14 +196,12 @@ if (refnorm == "SCTransform") {
         gc()
     }
 }
-rm(sobj)
-gc()
 
 # Find anchors between query and reference
 log_info("- Finding anchors")
 findtransferanchors_args$reference = reference
 if (is.null(split_by)) {
-    findtransferanchors_args$query = query
+    findtransferanchors_args$query = sobj
     anchors = do_call(FindTransferAnchors, findtransferanchors_args)
     findtransferanchors_args$reference = NULL
     findtransferanchors_args$query = NULL
@@ -196,7 +209,7 @@ if (is.null(split_by)) {
     gc()
 } else {
     anchors = mclapply(
-        X = query,
+        X = sobj,
         FUN = function(x) {
             findtransferanchors_args$query = x
             do_call(FindTransferAnchors, findtransferanchors_args)
@@ -212,25 +225,25 @@ if (is.null(split_by)) {
 log_info("- Mapping query to reference")
 mapquery_args$reference = reference
 if (is.null(split_by)) {
-    mapquery_args$query = query
+    mapquery_args$query = sobj
     mapquery_args$anchorset = anchors
-    query = do_call(MapQuery, mapquery_args)
+    sobj = do_call(MapQuery, mapquery_args)
     mapquery_args$reference = NULL
     mapquery_args$query = NULL
     mapquery_args$anchorset = NULL
     gc()
 } else {
-    query = mclapply(
-        X = seq_along(query),
+    sobj = mclapply(
+        X = seq_along(sobj),
         FUN = function(i) {
-            mapquery_args$query = query[[i]]
+            mapquery_args$query = sobj[[i]]
             mapquery_args$anchorset = anchors[[i]]
             do_call(MapQuery, mapquery_args)
         },
         mc.cores = ncores
     )
-    if (any(unlist(lapply(query, class)) == "try-error")) {
-        stop(paste0("\nmclapply (MapQuery) error:", query))
+    if (any(unlist(lapply(sobj, class)) == "try-error")) {
+        stop(paste0("\nmclapply (MapQuery) error:", sobj))
     }
 }
 
@@ -254,7 +267,7 @@ if (is.null(split_by)) {
     gc()
 } else {
     mappingscore = mclapply(
-        X = seq_along(query),
+        X = seq_along(sobj),
         FUN = function(i) {
             mappingscore_args$anchors = anchors[[i]]
             tryCatch({
@@ -274,25 +287,25 @@ if (is.null(split_by)) {
 # Calculate mapping score and add to metadata
 log_info("- Adding mapping score to metadata")
 if (is.null(split_by)) {
-    query = AddMetaData(
-        object = query,
+    sobj = AddMetaData(
+        object = sobj,
         metadata = mappingscore,
         col.name = "mapping.score"
     )
 } else {
-    query = mclapply(
-        X = seq_along(query),
+    sobj = mclapply(
+        X = seq_along(sobj),
         FUN = function(i) {
             AddMetaData(
-                object = query[[i]],
+                object = sobj[[i]],
                 metadata = mappingscore[[i]],
                 col.name = "mapping.score"
             )
         },
         mc.cores = ncores
     )
-    if (any(unlist(lapply(query, class)) == "try-error")) {
-        stop(paste0("\nmclapply (AddMetaData) error:", query))
+    if (any(unlist(lapply(sobj, class)) == "try-error")) {
+        stop(paste0("\nmclapply (AddMetaData) error:", sobj))
     }
 
     # Combine the results
@@ -300,19 +313,33 @@ if (is.null(split_by)) {
     gc()
     # Memory efficient way to merge the results
     # query = Reduce(function(x, y) merge(x, y, merge.dr = "ref.umap"), query)
-    query = merge(query[[1]], query[2:length(query)], merge.dr = "ref.umap")
+    sobj = merge(sobj[[1]], sobj[2:length(sobj)], merge.dr = "ref.umap")
 }
 
 # Add the alias to the metadata for the clusters
 log_info("- Adding ident to metadata and set as ident")
-query@meta.data = query@meta.data %>% mutate(
+sobj@meta.data = sobj@meta.data %>% mutate(
     !!sym(ident) := as.factor(!!parse_expr(paste0("predicted.", use)))
 )
-Idents(query) = ident
+Idents(sobj) = ident
+
+# Check if PrepSCTFindMarkers is done
+if (.is_sct(sobj) && is.null(sobj@commands$PrepSCTFindMarkers)) {
+    log_info("- Running PrepSCTFindMarkers ...")
+    sobj <- PrepSCTFindMarkers(sobj)
+    # compose a new SeuratCommand to record it to sobj@commands
+    commands <- names(pbmc_small@commands)
+    scommand <- pbmc_small@commands[[commands[length(commands)]]]
+    scommand@time.stamp <- Sys.time()
+    scommand@assay.used <- DefaultAssay(sobj)
+    scommand@call.string <- "PrepSCTFindMarkers(object = sobj)"
+    scommand@params <- list()
+    sobj@commands$PrepSCTFindMarkers <- scommand
+}
 
 # Save
 log_info("- Saving result ...")
-saveRDS(query, file = outfile)
+saveRDS(sobj, file = outfile)
 
 
 # ############################
@@ -325,7 +352,7 @@ ref.reduction = mapquery_args$reduction.model %||% "wnn.umap"
 for (qname in names(mapquery_args$refdata)) {
     rname <- mapquery_args$refdata[[qname]]
 
-    if (grepl("Array", class(reference[[rname]])) && grepl("Array", class(query[[qname]]))) {
+    if (grepl("Array", class(reference[[rname]])) && grepl("Array", class(sobj[[qname]]))) {
         log_warn("  Skipping transferred array: {qname} -> {rname}")
         next
     }
@@ -342,7 +369,7 @@ for (qname in names(mapquery_args$refdata)) {
     ) + NoLegend()
 
     query_p <- DimPlot(
-        object = query,
+        object = sobj,
         reduction = "ref.umap",
         group.by = paste0("predicted.", qname),
         label = TRUE,

{biopipen-0.30.0 → biopipen-0.31.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.30.0"
+version = "0.31.1"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"
@@ -11,14 +11,14 @@ generate-setup-file = true
 [tool.poetry.dependencies]
 python = "^3.9"
 # # required by other plugins
-# pipen = "^0.14"
-pipen-filters = "^0.13"
-pipen-cli-run = "^0.13"
-pipen-verbose = "^0.11"
-pipen-poplog = "^0.1.2"
+# pipen = "^0.15"
+pipen-filters = "^0.14"
+pipen-cli-run = "^0.14"
+pipen-verbose = "^0.12"
+pipen-poplog = "^0.2.0"
 datar = { version = "^0.15.6", extras = ["pandas"] }
-pipen-board = { version = "^0.15", extras = ["report"] }
-pipen-runinfo = { version = "^0.6", optional = true }
+pipen-board = { version = "^0.16", extras = ["report"] }
+pipen-runinfo = { version = "^0.7", optional = true }
 
 [tool.poetry.extras]
 runinfo = ["pipen-runinfo"]
@@ -55,5 +55,5 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.black]
 line-length = 88
-target-version = ['py38', 'py39', 'py310', 'py311']
+target-version = ['py39', 'py310', 'py311', 'py312']
 include = '\.pyi?$'

{biopipen-0.30.0 → biopipen-0.31.1}/setup.py

@@ -46,14 +46,14 @@ package_data = \
 
 install_requires = \
 ['datar[pandas]>=0.15.6,<0.16.0',
- 'pipen-board[report]>=0.15,<0.16',
- 'pipen-cli-run>=0.13,<0.14',
- 'pipen-filters>=0.13,<0.14',
- 'pipen-poplog>=0.1.2,<0.2.0',
- 'pipen-verbose>=0.11,<0.12']
+ 'pipen-board[report]>=0.16,<0.17',
+ 'pipen-cli-run>=0.14,<0.15',
+ 'pipen-filters>=0.14,<0.15',
+ 'pipen-poplog>=0.2.0,<0.3.0',
+ 'pipen-verbose>=0.12,<0.13']
 
 extras_require = \
-{'runinfo': ['pipen-runinfo>=0.6,<0.7']}
+{'runinfo': ['pipen-runinfo>=0.7,<0.8']}
 
 entry_points = \
 {'pipen_cli_run': ['bam = biopipen.ns.bam',
@@ -82,7 +82,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.30.0',
+    'version': '0.31.1',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.30.0/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.30.0"